GenericScatteringCalculator.py @ 378e808

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since 378e808 was 53c771e, checked in by Piotr Rozyczko <rozyczko@…>, 7 years ago
Converted unit tests
Property mode set to `100644`
File size: 33.4 KB

Rev	Line
[dc5ef15]	1	import sys
	2	import os
	3	import numpy
	4	import logging
	5	import time
	6
[4992ff2]	7	from PyQt5 import QtCore
	8	from PyQt5 import QtGui
	9	from PyQt5 import QtWidgets
	10
[dc5ef15]	11	from twisted.internet import threads
	12
	13	import sas.qtgui.Utilities.GuiUtils as GuiUtils
	14	from sas.qtgui.Utilities.GenericReader import GenReader
	15	from sas.sascalc.dataloader.data_info import Detector
	16	from sas.sascalc.dataloader.data_info import Source
	17	from sas.sascalc.calculator import sas_gen
	18	from sas.qtgui.Plotting.PlotterBase import PlotterBase
	19	from sas.qtgui.Plotting.Plotter2D import Plotter2D
	20	from sas.qtgui.Plotting.Plotter import Plotter
[fef38e8]	21
[dc5ef15]	22	from sas.qtgui.Plotting.PlotterData import Data1D
	23	from sas.qtgui.Plotting.PlotterData import Data2D
	24
	25	# Local UI
[b3e8629]	26	from .UI.GenericScatteringCalculator import Ui_GenericScatteringCalculator
[dc5ef15]	27
	28	_Q1D_MIN = 0.001
	29
	30
[4992ff2]	31	class GenericScatteringCalculator(QtWidgets.QDialog, Ui_GenericScatteringCalculator):
[dc5ef15]	32
	33	trigger_plot_3d = QtCore.pyqtSignal()
	34
	35	def __init__(self, parent=None):
	36	super(GenericScatteringCalculator, self).__init__()
	37	self.setupUi(self)
	38	self.manager = parent
	39	self.communicator = self.manager.communicator()
	40	self.model = sas_gen.GenSAS()
	41	self.omf_reader = sas_gen.OMFReader()
	42	self.sld_reader = sas_gen.SLDReader()
	43	self.pdb_reader = sas_gen.PDBReader()
	44	self.reader = None
	45	self.sld_data = None
	46
	47	self.parameters = []
	48	self.data = None
	49	self.datafile = None
	50	self.file_name = ''
	51	self.ext = None
	52	self.default_shape = str(self.cbShape.currentText())
	53	self.is_avg = False
	54	self.data_to_plot = None
[4d1eff2]	55	self.graph_num = 1 # index for name of graph
[dc5ef15]	56
	57	# combox box
	58	self.cbOptionsCalc.setVisible(False)
	59
	60	# push buttons
	61	self.cmdClose.clicked.connect(self.accept)
	62	self.cmdHelp.clicked.connect(self.onHelp)
	63
	64	self.cmdLoad.clicked.connect(self.loadFile)
	65	self.cmdCompute.clicked.connect(self.onCompute)
	66	self.cmdReset.clicked.connect(self.onReset)
	67	self.cmdSave.clicked.connect(self.onSaveFile)
	68
	69	self.cmdDraw.clicked.connect(lambda: self.plot3d(has_arrow=True))
	70	self.cmdDrawpoints.clicked.connect(lambda: self.plot3d(has_arrow=False))
	71
	72	# validators
	73	# scale, volume and background must be positive
	74	validat_regex_pos = QtCore.QRegExp('^[+]?([.]\d+\|\d+([.]\d+)?)$')
	75	self.txtScale.setValidator(QtGui.QRegExpValidator(validat_regex_pos,
	76	self.txtScale))
	77	self.txtBackground.setValidator(QtGui.QRegExpValidator(
	78	validat_regex_pos, self.txtBackground))
	79	self.txtTotalVolume.setValidator(QtGui.QRegExpValidator(
	80	validat_regex_pos, self.txtTotalVolume))
	81
	82	# fraction of spin up between 0 and 1
	83	validat_regexbetween0_1 = QtCore.QRegExp('^(0(\.\d)\|1(\.0+)?)$')
	84	self.txtUpFracIn.setValidator(
	85	QtGui.QRegExpValidator(validat_regexbetween0_1, self.txtUpFracIn))
	86	self.txtUpFracOut.setValidator(
	87	QtGui.QRegExpValidator(validat_regexbetween0_1, self.txtUpFracOut))
	88
	89	# 0 < Qmax <= 1000
	90	validat_regex_q = QtCore.QRegExp('^1000$\|^[+]?(\d{1,3}([.]\d+)?)$')
	91	self.txtQxMax.setValidator(QtGui.QRegExpValidator(validat_regex_q,
	92	self.txtQxMax))
	93	self.txtQxMax.textChanged.connect(self.check_value)
	94
	95	# 2 <= Qbin <= 1000
	96	self.txtNoQBins.setValidator(QtGui.QRegExpValidator(validat_regex_q,
	97	self.txtNoQBins))
	98	self.txtNoQBins.textChanged.connect(self.check_value)
	99
	100	# plots - 3D in real space
[4d1eff2]	101	self.trigger_plot_3d.connect(lambda: self.plot3d(has_arrow=False))
[dc5ef15]	102
	103	# TODO the option Ellipsoid has not been implemented
	104	self.cbShape.currentIndexChanged.connect(self.selectedshapechange)
	105
[457d961]	106	# New font to display angstrom symbol
	107	new_font = 'font-family: -apple-system, "Helvetica Neue", "Ubuntu";'
	108	self.lblUnitSolventSLD.setStyleSheet(new_font)
	109	self.lblUnitVolume.setStyleSheet(new_font)
	110	self.lbl5.setStyleSheet(new_font)
	111	self.lblUnitMx.setStyleSheet(new_font)
	112	self.lblUnitMy.setStyleSheet(new_font)
	113	self.lblUnitMz.setStyleSheet(new_font)
	114	self.lblUnitNucl.setStyleSheet(new_font)
	115	self.lblUnitx.setStyleSheet(new_font)
	116	self.lblUnity.setStyleSheet(new_font)
	117	self.lblUnitz.setStyleSheet(new_font)
	118
[dc5ef15]	119	def selectedshapechange(self):
	120	"""
	121	TODO Temporary solution to display information about option 'Ellipsoid'
	122	"""
[b3e8629]	123	print("The option Ellipsoid has not been implemented yet.")
[dc5ef15]	124	self.communicator.statusBarUpdateSignal.emit(
	125	"The option Ellipsoid has not been implemented yet.")
	126
	127	def loadFile(self):
	128	"""
	129	Open menu to choose the datafile to load
	130	Only extensions .SLD, .PDB, .OMF, .sld, .pdb, .omf
	131	"""
	132	try:
[4992ff2]	133	self.datafile = QtWidgets.QFileDialog.getOpenFileName(
[dc5ef15]	134	self, "Choose a file", "", "All Gen files (.OMF .omf) ;;"
	135	"SLD files (.SLD .sld);;PDB files (.pdb .PDB);; "
	136	"OMF files (.OMF .omf);; "
[fbfc488]	137	"All files (.)")[0]
[dc5ef15]	138	if self.datafile:
	139	self.default_shape = str(self.cbShape.currentText())
	140	self.file_name = os.path.basename(str(self.datafile))
	141	self.ext = os.path.splitext(str(self.datafile))[1]
	142	if self.ext in self.omf_reader.ext:
	143	loader = self.omf_reader
	144	elif self.ext in self.sld_reader.ext:
	145	loader = self.sld_reader
	146	elif self.ext in self.pdb_reader.ext:
	147	loader = self.pdb_reader
	148	else:
	149	loader = None
	150	# disable some entries depending on type of loaded file
	151	# (according to documentation)
	152	if self.ext.lower() in ['.sld', '.omf', '.pdb']:
	153	self.txtUpFracIn.setEnabled(False)
	154	self.txtUpFracOut.setEnabled(False)
	155	self.txtUpTheta.setEnabled(False)
	156
	157	if self.reader is not None and self.reader.isrunning():
	158	self.reader.stop()
	159	self.cmdLoad.setEnabled(False)
	160	self.cmdLoad.setText('Loading...')
	161	self.communicator.statusBarUpdateSignal.emit(
	162	"Loading File {}".format(os.path.basename(
	163	str(self.datafile))))
	164	self.reader = GenReader(path=str(self.datafile), loader=loader,
	165	completefn=self.complete_loading,
	166	updatefn=self.load_update)
	167	self.reader.queue()
	168	except (RuntimeError, IOError):
[b3e8629]	169	log_msg = "Generic SAS Calculator: %s" % sys.exc_info()[1]
[dc5ef15]	170	logging.info(log_msg)
	171	raise
	172	return
	173
	174	def load_update(self):
	175	""" Legacy function used in GenRead """
	176	if self.reader.isrunning():
	177	status_type = "progress"
	178	else:
	179	status_type = "stop"
	180	logging.info(status_type)
	181
	182	def complete_loading(self, data=None):
	183	""" Function used in GenRead"""
	184	self.cbShape.setEnabled(False)
	185	try:
	186	is_pdbdata = False
	187	self.txtData.setText(os.path.basename(str(self.datafile)))
	188	self.is_avg = False
	189	if self.ext in self.omf_reader.ext:
	190	gen = sas_gen.OMF2SLD()
	191	gen.set_data(data)
	192	self.sld_data = gen.get_magsld()
	193	self.check_units()
	194	elif self.ext in self.sld_reader.ext:
	195	self.sld_data = data
	196	elif self.ext in self.pdb_reader.ext:
	197	self.sld_data = data
	198	is_pdbdata = True
	199	# Display combobox of orientation only for pdb data
	200	self.cbOptionsCalc.setVisible(is_pdbdata)
	201	self.update_gui()
	202	except IOError:
	203	log_msg = "Loading Error: " \
	204	"This file format is not supported for GenSAS."
	205	logging.info(log_msg)
	206	raise
	207	except ValueError:
	208	log_msg = "Could not find any data"
	209	logging.info(log_msg)
	210	raise
	211	logging.info("Load Complete")
	212	self.cmdLoad.setEnabled(True)
	213	self.cmdLoad.setText('Load')
	214	self.trigger_plot_3d.emit()
	215
	216	def check_units(self):
	217	"""
	218	Check if the units from the OMF file correspond to the default ones
	219	displayed on the interface.
	220	If not, modify the GUI with the correct unit
	221	"""
	222	# TODO: adopt the convention of font and symbol for the updated values
	223	if sas_gen.OMFData().valueunit != 'A^(-2)':
	224	value_unit = sas_gen.OMFData().valueunit
	225	self.lbl_unitMx.setText(value_unit)
	226	self.lbl_unitMy.setText(value_unit)
	227	self.lbl_unitMz.setText(value_unit)
	228	self.lbl_unitNucl.setText(value_unit)
	229	if sas_gen.OMFData().meshunit != 'A':
	230	mesh_unit = sas_gen.OMFData().meshunit
	231	self.lbl_unitx.setText(mesh_unit)
	232	self.lbl_unity.setText(mesh_unit)
	233	self.lbl_unitz.setText(mesh_unit)
	234	self.lbl_unitVolume.setText(mesh_unit+"^3")
	235
	236	def check_value(self):
	237	"""Check range of text edits for QMax and Number of Qbins """
	238	text_edit = self.sender()
[7fb471d]	239	text_edit.setStyleSheet('background-color: rgb(255, 255, 255);')
[dc5ef15]	240	if text_edit.text():
	241	value = float(str(text_edit.text()))
	242	if text_edit == self.txtQxMax:
	243	if value <= 0 or value > 1000:
[7fb471d]	244	text_edit.setStyleSheet('background-color: rgb(255, 182, 193);')
[dc5ef15]	245	else:
[7fb471d]	246	text_edit.setStyleSheet('background-color: rgb(255, 255, 255);')
[dc5ef15]	247	elif text_edit == self.txtNoQBins:
	248	if value < 2 or value > 1000:
[7fb471d]	249	self.txtNoQBins.setStyleSheet('background-color: rgb(255, 182, 193);')
[dc5ef15]	250	else:
[7fb471d]	251	self.txtNoQBins.setStyleSheet('background-color: rgb(255, 255, 255);')
[dc5ef15]	252
	253	def update_gui(self):
	254	""" Update the interface with values from loaded data """
	255	self.model.set_is_avg(self.is_avg)
	256	self.model.set_sld_data(self.sld_data)
	257	self.model.params['total_volume'] = len(self.sld_data.sld_n)*self.sld_data.vol_pix[0]
	258
	259	# add condition for activation of save button
	260	self.cmdSave.setEnabled(True)
	261
	262	# activation of 3D plots' buttons (with and without arrows)
	263	self.cmdDraw.setEnabled(self.sld_data is not None)
	264	self.cmdDrawpoints.setEnabled(self.sld_data is not None)
	265
	266	self.txtScale.setText(str(self.model.params['scale']))
	267	self.txtBackground.setText(str(self.model.params['background']))
	268	self.txtSolventSLD.setText(str(self.model.params['solvent_SLD']))
	269
	270	# Volume to write to interface: npts x volume of first pixel
	271	self.txtTotalVolume.setText(str(len(self.sld_data.sld_n)*self.sld_data.vol_pix[0]))
	272
	273	self.txtUpFracIn.setText(str(self.model.params['Up_frac_in']))
	274	self.txtUpFracOut.setText(str(self.model.params['Up_frac_out']))
	275	self.txtUpTheta.setText(str(self.model.params['Up_theta']))
	276
	277	self.txtNoPixels.setText(str(len(self.sld_data.sld_n)))
	278	self.txtNoPixels.setEnabled(False)
	279
	280	list_parameters = ['sld_mx', 'sld_my', 'sld_mz', 'sld_n', 'xnodes',
	281	'ynodes', 'znodes', 'xstepsize', 'ystepsize',
	282	'zstepsize']
	283	list_gui_button = [self.txtMx, self.txtMy, self.txtMz, self.txtNucl,
	284	self.txtXnodes, self.txtYnodes, self.txtZnodes,
	285	self.txtXstepsize, self.txtYstepsize,
	286	self.txtZstepsize]
	287
	288	# Fill right hand side of GUI
	289	for indx, item in enumerate(list_parameters):
	290	if getattr(self.sld_data, item) is None:
	291	list_gui_button[indx].setText('NaN')
	292	else:
	293	value = getattr(self.sld_data, item)
	294	if isinstance(value, numpy.ndarray):
	295	item_for_gui = str(GuiUtils.formatNumber(numpy.average(value), True))
	296	else:
	297	item_for_gui = str(GuiUtils.formatNumber(value, True))
	298	list_gui_button[indx].setText(item_for_gui)
	299
	300	# Enable / disable editing of right hand side of GUI
	301	for indx, item in enumerate(list_parameters):
	302	if indx < 4:
	303	# this condition only applies to Mx,y,z and Nucl
	304	value = getattr(self.sld_data, item)
	305	enable = self.sld_data.pix_type == 'pixel' \
	306	and numpy.min(value) == numpy.max(value)
	307	else:
	308	enable = not self.sld_data.is_data
	309	list_gui_button[indx].setEnabled(enable)
	310
	311	def write_new_values_from_gui(self):
	312	"""
	313	update parameters using modified inputs from GUI
	314	used before computing
	315	"""
	316	if self.txtScale.isModified():
	317	self.model.params['scale'] = float(self.txtScale.text())
	318
	319	if self.txtBackground.isModified():
	320	self.model.params['background'] = float(self.txtBackground.text())
	321
	322	if self.txtSolventSLD.isModified():
	323	self.model.params['solvent_SLD'] = float(self.txtSolventSLD.text())
	324
	325	# Different condition for total volume to get correct volume after
	326	# applying set_sld_data in compute
	327	if self.txtTotalVolume.isModified() \
	328	or self.model.params['total_volume'] != float(self.txtTotalVolume.text()):
	329	self.model.params['total_volume'] = float(self.txtTotalVolume.text())
	330
	331	if self.txtUpFracIn.isModified():
	332	self.model.params['Up_frac_in'] = float(self.txtUpFracIn.text())
	333
	334	if self.txtUpFracOut.isModified():
	335	self.model.params['Up_frac_out'] = float(self.txtUpFracOut.text())
	336
	337	if self.txtUpTheta.isModified():
	338	self.model.params['Up_theta'] = float(self.txtUpTheta.text())
	339
	340	if self.txtMx.isModified():
	341	self.sld_data.sld_mx = float(self.txtMx.text())*\
	342	numpy.ones(len(self.sld_data.sld_mx))
	343
	344	if self.txtMy.isModified():
	345	self.sld_data.sld_my = float(self.txtMy.text())*\
	346	numpy.ones(len(self.sld_data.sld_my))
	347
	348	if self.txtMz.isModified():
	349	self.sld_data.sld_mz = float(self.txtMz.text())*\
	350	numpy.ones(len(self.sld_data.sld_mz))
	351
	352	if self.txtNucl.isModified():
	353	self.sld_data.sld_n = float(self.txtNucl.text())*\
	354	numpy.ones(len(self.sld_data.sld_n))
	355
	356	if self.txtXnodes.isModified():
	357	self.sld_data.xnodes = int(self.txtXnodes.text())
	358
	359	if self.txtYnodes.isModified():
	360	self.sld_data.ynodes = int(self.txtYnodes.text())
	361
	362	if self.txtZnodes.isModified():
	363	self.sld_data.znodes = int(self.txtZnodes.text())
	364
	365	if self.txtXstepsize.isModified():
	366	self.sld_data.xstepsize = float(self.txtXstepsize.text())
	367
	368	if self.txtYstepsize.isModified():
	369	self.sld_data.ystepsize = float(self.txtYstepsize.text())
	370
	371	if self.txtZstepsize.isModified():
	372	self.sld_data.zstepsize = float(self.txtZstepsize.text())
	373
	374	if self.cbOptionsCalc.isVisible():
	375	self.is_avg = (self.cbOptionsCalc.currentIndex() == 1)
	376
	377	def onHelp(self):
	378	"""
	379	Bring up the Generic Scattering calculator Documentation whenever
	380	the HELP button is clicked.
	381	Calls Documentation Window with the path of the location within the
	382	documentation tree (after /doc/ ....".
	383	"""
	384	try:
[b0c5e8c]	385	location = GuiUtils.HELP_DIRECTORY_LOCATION + \
[dc5ef15]	386	"/user/sasgui/perspectives/calculator/sas_calculator_help.html"
	387	self.manager._helpView.load(QtCore.QUrl(location))
	388	self.manager._helpView.show()
	389	except AttributeError:
	390	# No manager defined - testing and standalone runs
	391	pass
	392
	393	def onReset(self):
	394	""" Reset the inputs of textEdit to default values """
	395	try:
	396	# reset values in textedits
	397	self.txtUpFracIn.setText("1.0")
	398	self.txtUpFracOut.setText("1.0")
	399	self.txtUpTheta.setText("0.0")
	400	self.txtBackground.setText("0.0")
	401	self.txtScale.setText("1.0")
	402	self.txtSolventSLD.setText("0.0")
	403	self.txtTotalVolume.setText("216000.0")
	404	self.txtNoQBins.setText("50")
	405	self.txtQxMax.setText("0.3")
	406	self.txtNoPixels.setText("1000")
	407	self.txtMx.setText("0")
	408	self.txtMy.setText("0")
	409	self.txtMz.setText("0")
	410	self.txtNucl.setText("6.97e-06")
	411	self.txtXnodes.setText("10")
	412	self.txtYnodes.setText("10")
	413	self.txtZnodes.setText("10")
	414	self.txtXstepsize.setText("6")
	415	self.txtYstepsize.setText("6")
	416	self.txtZstepsize.setText("6")
	417	# reset Load button and textedit
	418	self.txtData.setText('Default SLD Profile')
	419	self.cmdLoad.setEnabled(True)
	420	self.cmdLoad.setText('Load')
	421	# reset option for calculation
	422	self.cbOptionsCalc.setCurrentIndex(0)
	423	self.cbOptionsCalc.setVisible(False)
	424	# reset shape button
	425	self.cbShape.setCurrentIndex(0)
	426	self.cbShape.setEnabled(True)
	427	# reset compute button
	428	self.cmdCompute.setText('Compute')
	429	self.cmdCompute.setEnabled(True)
	430	# TODO reload default data set
	431	self._create_default_sld_data()
	432
	433	finally:
	434	pass
	435
	436	def _create_default_2d_data(self):
	437	"""
	438	Copied from previous version
	439	Create 2D data by default
	440	:warning: This data is never plotted.
	441	"""
	442	self.qmax_x = float(self.txtQxMax.text())
	443	self.npts_x = int(self.txtNoQBins.text())
	444	self.data = Data2D()
	445	self.data.is_data = False
	446	# # Default values
	447	self.data.detector.append(Detector())
	448	index = len(self.data.detector) - 1
	449	self.data.detector[index].distance = 8000 # mm
	450	self.data.source.wavelength = 6 # A
	451	self.data.detector[index].pixel_size.x = 5 # mm
	452	self.data.detector[index].pixel_size.y = 5 # mm
	453	self.data.detector[index].beam_center.x = self.qmax_x
	454	self.data.detector[index].beam_center.y = self.qmax_x
	455	xmax = self.qmax_x
	456	xmin = -xmax
	457	ymax = self.qmax_x
	458	ymin = -ymax
	459	qstep = self.npts_x
	460
	461	x = numpy.linspace(start=xmin, stop=xmax, num=qstep, endpoint=True)
	462	y = numpy.linspace(start=ymin, stop=ymax, num=qstep, endpoint=True)
	463	# use data info instead
	464	new_x = numpy.tile(x, (len(y), 1))
	465	new_y = numpy.tile(y, (len(x), 1))
	466	new_y = new_y.swapaxes(0, 1)
	467	# all data require now in 1d array
	468	qx_data = new_x.flatten()
	469	qy_data = new_y.flatten()
	470	q_data = numpy.sqrt(qx_data * qx_data + qy_data * qy_data)
	471	# set all True (standing for unmasked) as default
	472	mask = numpy.ones(len(qx_data), dtype=bool)
	473	self.data.source = Source()
	474	self.data.data = numpy.ones(len(mask))
	475	self.data.err_data = numpy.ones(len(mask))
	476	self.data.qx_data = qx_data
	477	self.data.qy_data = qy_data
	478	self.data.q_data = q_data
	479	self.data.mask = mask
	480	# store x and y bin centers in q space
	481	self.data.x_bins = x
	482	self.data.y_bins = y
	483	# max and min taking account of the bin sizes
	484	self.data.xmin = xmin
	485	self.data.xmax = xmax
	486	self.data.ymin = ymin
	487	self.data.ymax = ymax
	488
	489	def _create_default_sld_data(self):
	490	"""
	491	Copied from previous version
	492	Making default sld-data
	493	"""
	494	sld_n_default = 6.97e-06 # what is this number??
	495	omfdata = sas_gen.OMFData()
	496	omf2sld = sas_gen.OMF2SLD()
	497	omf2sld.set_data(omfdata, self.default_shape)
	498	self.sld_data = omf2sld.output
	499	self.sld_data.is_data = False
	500	self.sld_data.filename = "Default SLD Profile"
	501	self.sld_data.set_sldn(sld_n_default)
	502
	503	def _create_default_1d_data(self):
	504	"""
	505	Copied from previous version
	506	Create 1D data by default
	507	:warning: This data is never plotted.
	508	residuals.x = data_copy.x[index]
	509	residuals.dy = numpy.ones(len(residuals.y))
	510	residuals.dx = None
	511	residuals.dxl = None
	512	residuals.dxw = None
	513	"""
	514	self.qmax_x = float(self.txtQxMax.text())
	515	self.npts_x = int(self.txtNoQBins.text())
	516	# Default values
	517	xmax = self.qmax_x
	518	xmin = self.qmax_x * _Q1D_MIN
	519	qstep = self.npts_x
	520	x = numpy.linspace(start=xmin, stop=xmax, num=qstep, endpoint=True)
	521	# store x and y bin centers in q space
	522	y = numpy.ones(len(x))
	523	dy = numpy.zeros(len(x))
	524	dx = numpy.zeros(len(x))
	525	self.data = Data1D(x=x, y=y)
	526	self.data.dx = dx
	527	self.data.dy = dy
	528
	529	def onCompute(self):
	530	"""
	531	Copied from previous version
	532	Execute the computation of I(qx, qy)
	533	"""
	534	# Set default data when nothing loaded yet
	535	if self.sld_data is None:
	536	self._create_default_sld_data()
	537	try:
	538	self.model.set_sld_data(self.sld_data)
	539	self.write_new_values_from_gui()
	540	if self.is_avg or self.is_avg is None:
	541	self._create_default_1d_data()
	542	i_out = numpy.zeros(len(self.data.y))
	543	inputs = [self.data.x, [], i_out]
	544	else:
	545	self._create_default_2d_data()
	546	i_out = numpy.zeros(len(self.data.data))
	547	inputs = [self.data.qx_data, self.data.qy_data, i_out]
	548	logging.info("Computation is in progress...")
	549	self.cmdCompute.setText('Wait...')
	550	self.cmdCompute.setEnabled(False)
	551	d = threads.deferToThread(self.complete, inputs, self._update)
	552	# Add deferred callback for call return
	553	d.addCallback(self.plot_1_2d)
[7fb471d]	554	d.addErrback(self.calculateFailed)
[dc5ef15]	555	except:
[b3e8629]	556	log_msg = "{}. stop".format(sys.exc_info()[1])
[dc5ef15]	557	logging.info(log_msg)
	558	return
	559
	560	def _update(self, value):
	561	"""
	562	Copied from previous version
	563	"""
	564	pass
	565
[7fb471d]	566	def calculateFailed(self, reason):
	567	"""
	568	"""
	569	print("Calculate Failed with:\n", reason)
	570	pass
	571
[dc5ef15]	572	def complete(self, input, update=None):
	573	"""
	574	Gen compute complete function
	575	:Param input: input list [qx_data, qy_data, i_out]
	576	"""
	577	out = numpy.empty(0)
	578	for ind in range(len(input[0])):
	579	if self.is_avg:
	580	if ind % 1 == 0 and update is not None:
	581	# update()
	582	percentage = int(100.0 * float(ind) / len(input[0]))
	583	update(percentage)
	584	time.sleep(0.001) # 0.1
	585	inputi = [input[0][ind:ind + 1], [], input[2][ind:ind + 1]]
	586	outi = self.model.run(inputi)
	587	out = numpy.append(out, outi)
	588	else:
	589	if ind % 50 == 0 and update is not None:
	590	percentage = int(100.0 * float(ind) / len(input[0]))
	591	update(percentage)
	592	time.sleep(0.001)
	593	inputi = [input[0][ind:ind + 1], input[1][ind:ind + 1],
	594	input[2][ind:ind + 1]]
	595	outi = self.model.runXY(inputi)
	596	out = numpy.append(out, outi)
	597	self.data_to_plot = out
	598	logging.info('Gen computation completed.')
	599	self.cmdCompute.setText('Compute')
	600	self.cmdCompute.setEnabled(True)
	601	return
	602
	603	def onSaveFile(self):
	604	"""Save data as .sld file"""
	605	path = os.path.dirname(str(self.datafile))
	606	default_name = os.path.join(path, 'sld_file')
	607	kwargs = {
	608	'parent': self,
	609	'directory': default_name,
	610	'filter': 'SLD file (*.sld)',
[4992ff2]	611	'options': QtWidgets.QFileDialog.DontUseNativeDialog}
[dc5ef15]	612	# Query user for filename.
[d6b8a1d]	613	filename_tuple = QtWidgets.QFileDialog.getSaveFileName(**kwargs)
[53c771e]	614	filename = filename_tuple[0]
[dc5ef15]	615	if filename:
	616	try:
[d6b8a1d]	617	_, extension = os.path.splitext(filename)
	618	if not extension:
	619	filename = '.'.join((filename, 'sld'))
	620	sas_gen.SLDReader().write(filename, self.sld_data)
[dc5ef15]	621	except:
	622	raise
	623
	624	def plot3d(self, has_arrow=False):
	625	""" Generate 3D plot in real space with or without arrows """
	626	self.write_new_values_from_gui()
	627	graph_title = " Graph {}: {} 3D SLD Profile".format(self.graph_num,
	628	self.file_name)
	629	if has_arrow:
	630	graph_title += ' - Magnetic Vector as Arrow'
	631
	632	plot3D = Plotter3D(self, graph_title)
	633	plot3D.plot(self.sld_data, has_arrow=has_arrow)
	634	plot3D.show()
	635	self.graph_num += 1
	636
	637	def plot_1_2d(self, d):
	638	""" Generate 1D or 2D plot, called in Compute"""
	639	if self.is_avg or self.is_avg is None:
	640	data = Data1D(x=self.data.x, y=self.data_to_plot)
	641	data.title = "GenSAS {} #{} 1D".format(self.file_name,
	642	int(self.graph_num))
	643	data.xaxis('\\rm{Q_{x}}', '\AA^{-1}')
	644	data.yaxis('\\rm{Intensity}', 'cm^{-1}')
	645	plot1D = Plotter(self)
	646	plot1D.plot(data)
	647	plot1D.show()
	648	self.graph_num += 1
	649	# TODO
[b3e8629]	650	print('TRANSFER OF DATA TO MAIN PANEL TO BE IMPLEMENTED')
[dc5ef15]	651	return plot1D
	652	else:
	653	numpy.nan_to_num(self.data_to_plot)
	654	data = Data2D(image=self.data_to_plot,
	655	qx_data=self.data.qx_data,
	656	qy_data=self.data.qy_data,
	657	q_data=self.data.q_data,
	658	xmin=self.data.xmin, xmax=self.data.ymax,
	659	ymin=self.data.ymin, ymax=self.data.ymax,
	660	err_image=self.data.err_data)
	661	data.title = "GenSAS {} #{} 2D".format(self.file_name,
	662	int(self.graph_num))
	663	plot2D = Plotter2D(self)
	664	plot2D.plot(data)
	665	plot2D.show()
	666	self.graph_num += 1
	667	# TODO
[b3e8629]	668	print('TRANSFER OF DATA TO MAIN PANEL TO BE IMPLEMENTED')
[dc5ef15]	669	return plot2D
	670
	671
	672	class Plotter3DWidget(PlotterBase):
	673	"""
	674	3D Plot widget for use with a QDialog
	675	"""
	676	def __init__(self, parent=None, manager=None):
	677	super(Plotter3DWidget, self).__init__(parent, manager=manager)
	678
	679	@property
	680	def data(self):
	681	return self._data
	682
	683	@data.setter
	684	def data(self, data=None):
	685	""" data setter """
	686	self._data = data
	687
	688	def plot(self, data=None, has_arrow=False):
	689	"""
	690	Plot 3D self._data
	691	"""
[4d1eff2]	692	if not data:
	693	return
[dc5ef15]	694	self.data = data
[4d1eff2]	695	#assert(self._data)
[dc5ef15]	696	# Prepare and show the plot
	697	self.showPlot(data=self.data, has_arrow=has_arrow)
	698
	699	def showPlot(self, data, has_arrow=False):
	700	"""
	701	Render and show the current data
	702	"""
	703	# If we don't have any data, skip.
	704	if data is None:
	705	return
[fef38e8]	706	# This import takes forever - place it here so the main UI starts faster
	707	from mpl_toolkits.mplot3d import Axes3D
[dc5ef15]	708	color_dic = {'H': 'blue', 'D': 'purple', 'N': 'orange',
	709	'O': 'red', 'C': 'green', 'P': 'cyan', 'Other': 'k'}
	710	marker = ','
	711	m_size = 2
	712
	713	pos_x = data.pos_x
	714	pos_y = data.pos_y
	715	pos_z = data.pos_z
	716	sld_mx = data.sld_mx
	717	sld_my = data.sld_my
	718	sld_mz = data.sld_mz
	719	pix_symbol = data.pix_symbol
	720	sld_tot = numpy.fabs(sld_mx) + numpy.fabs(sld_my) + \
	721	numpy.fabs(sld_mz) + numpy.fabs(data.sld_n)
	722	is_nonzero = sld_tot > 0.0
	723	is_zero = sld_tot == 0.0
	724
	725	if data.pix_type == 'atom':
	726	marker = 'o'
	727	m_size = 3.5
	728
	729	self.figure.clear()
	730	self.figure.subplots_adjust(left=0.1, right=.8, bottom=.1)
	731	ax = Axes3D(self.figure)
	732	ax.set_xlabel('x ($\A{}$)'.format(data.pos_unit))
	733	ax.set_ylabel('z ($\A{}$)'.format(data.pos_unit))
	734	ax.set_zlabel('y ($\A{}$)'.format(data.pos_unit))
	735
	736	# I. Plot null points
	737	if is_zero.any():
	738	im = ax.plot(pos_x[is_zero], pos_z[is_zero], pos_y[is_zero],
	739	marker, c="y", alpha=0.5, markeredgecolor='y',
	740	markersize=m_size)
	741	pos_x = pos_x[is_nonzero]
	742	pos_y = pos_y[is_nonzero]
	743	pos_z = pos_z[is_nonzero]
	744	sld_mx = sld_mx[is_nonzero]
	745	sld_my = sld_my[is_nonzero]
	746	sld_mz = sld_mz[is_nonzero]
	747	pix_symbol = data.pix_symbol[is_nonzero]
	748	# II. Plot selective points in color
	749	other_color = numpy.ones(len(pix_symbol), dtype='bool')
[b3e8629]	750	for key in list(color_dic.keys()):
[dc5ef15]	751	chosen_color = pix_symbol == key
	752	if numpy.any(chosen_color):
	753	other_color = other_color & (chosen_color!=True)
	754	color = color_dic[key]
	755	im = ax.plot(pos_x[chosen_color], pos_z[chosen_color],
	756	pos_y[chosen_color], marker, c=color, alpha=0.5,
	757	markeredgecolor=color, markersize=m_size, label=key)
	758	# III. Plot All others
	759	if numpy.any(other_color):
	760	a_name = ''
	761	if data.pix_type == 'atom':
	762	# Get atom names not in the list
	763	a_names = [symb for symb in pix_symbol \
[b3e8629]	764	if symb not in list(color_dic.keys())]
[dc5ef15]	765	a_name = a_names[0]
	766	for name in a_names:
	767	new_name = ", " + name
	768	if a_name.count(name) == 0:
	769	a_name += new_name
	770	# plot in black
	771	im = ax.plot(pos_x[other_color], pos_z[other_color],
	772	pos_y[other_color], marker, c="k", alpha=0.5,
	773	markeredgecolor="k", markersize=m_size, label=a_name)
	774	if data.pix_type == 'atom':
	775	ax.legend(loc='upper left', prop={'size': 10})
	776	# IV. Draws atomic bond with grey lines if any
	777	if data.has_conect:
	778	for ind in range(len(data.line_x)):
	779	im = ax.plot(data.line_x[ind], data.line_z[ind],
	780	data.line_y[ind], '-', lw=0.6, c="grey",
	781	alpha=0.3)
	782	# V. Draws magnetic vectors
	783	if has_arrow and len(pos_x) > 0:
	784	def _draw_arrow(input=None, update=None):
[fef38e8]	785	# import moved here for performance reasons
	786	from sas.qtgui.Plotting.Arrow3D import Arrow3D
[dc5ef15]	787	"""
	788	draw magnetic vectors w/arrow
	789	"""
	790	max_mx = max(numpy.fabs(sld_mx))
	791	max_my = max(numpy.fabs(sld_my))
	792	max_mz = max(numpy.fabs(sld_mz))
	793	max_m = max(max_mx, max_my, max_mz)
	794	try:
	795	max_step = max(data.xstepsize, data.ystepsize, data.zstepsize)
	796	except:
	797	max_step = 0
	798	if max_step <= 0:
	799	max_step = 5
	800	try:
	801	if max_m != 0:
	802	unit_x2 = sld_mx / max_m
	803	unit_y2 = sld_my / max_m
	804	unit_z2 = sld_mz / max_m
	805	# 0.8 is for avoiding the color becomes white=(1,1,1))
	806	color_x = numpy.fabs(unit_x2 * 0.8)
	807	color_y = numpy.fabs(unit_y2 * 0.8)
	808	color_z = numpy.fabs(unit_z2 * 0.8)
	809	x2 = pos_x + unit_x2 * max_step
	810	y2 = pos_y + unit_y2 * max_step
	811	z2 = pos_z + unit_z2 * max_step
	812	x_arrow = numpy.column_stack((pos_x, x2))
	813	y_arrow = numpy.column_stack((pos_y, y2))
	814	z_arrow = numpy.column_stack((pos_z, z2))
	815	colors = numpy.column_stack((color_x, color_y, color_z))
	816	arrows = Arrow3D(self.figure, x_arrow, z_arrow, y_arrow,
	817	colors, mutation_scale=10, lw=1,
	818	arrowstyle="->", alpha=0.5)
	819	ax.add_artist(arrows)
	820	except:
	821	pass
	822	log_msg = "Arrow Drawing completed.\n"
	823	logging.info(log_msg)
	824	log_msg = "Arrow Drawing is in progress..."
	825	logging.info(log_msg)
	826
	827	# Defer the drawing of arrows to another thread
	828	d = threads.deferToThread(_draw_arrow, ax)
	829
	830	self.figure.canvas.resizing = False
	831	self.figure.canvas.draw()
	832
	833
[4992ff2]	834	class Plotter3D(QtWidgets.QDialog, Plotter3DWidget):
[dc5ef15]	835	def __init__(self, parent=None, graph_title=''):
	836	self.graph_title = graph_title
[4992ff2]	837	QtWidgets.QDialog.__init__(self)
[dc5ef15]	838	Plotter3DWidget.__init__(self, manager=parent)
	839	self.setWindowTitle(self.graph_title)
	840

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SasView

source: sasview/src/sas/qtgui/Calculators/GenericScatteringCalculator.py @ 378e808

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