GenericScatteringCalculator.py @ aefde77

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 aefde77 was e90988c, checked in by Piotr Rozyczko <rozyczko@…>, 7 years ago
Show help pages in default browser. Fixed some help links and modified unit tests. SASVIEW-800
Property mode set to `100644`
File size: 33.2 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	"""
[e90988c]	384	location = "/user/sasgui/perspectives/calculator/sas_calculator_help.html"
	385	self.manager.showHelp(location)
[dc5ef15]	386
	387	def onReset(self):
	388	""" Reset the inputs of textEdit to default values """
	389	try:
	390	# reset values in textedits
	391	self.txtUpFracIn.setText("1.0")
	392	self.txtUpFracOut.setText("1.0")
	393	self.txtUpTheta.setText("0.0")
	394	self.txtBackground.setText("0.0")
	395	self.txtScale.setText("1.0")
	396	self.txtSolventSLD.setText("0.0")
	397	self.txtTotalVolume.setText("216000.0")
	398	self.txtNoQBins.setText("50")
	399	self.txtQxMax.setText("0.3")
	400	self.txtNoPixels.setText("1000")
	401	self.txtMx.setText("0")
	402	self.txtMy.setText("0")
	403	self.txtMz.setText("0")
	404	self.txtNucl.setText("6.97e-06")
	405	self.txtXnodes.setText("10")
	406	self.txtYnodes.setText("10")
	407	self.txtZnodes.setText("10")
	408	self.txtXstepsize.setText("6")
	409	self.txtYstepsize.setText("6")
	410	self.txtZstepsize.setText("6")
	411	# reset Load button and textedit
	412	self.txtData.setText('Default SLD Profile')
	413	self.cmdLoad.setEnabled(True)
	414	self.cmdLoad.setText('Load')
	415	# reset option for calculation
	416	self.cbOptionsCalc.setCurrentIndex(0)
	417	self.cbOptionsCalc.setVisible(False)
	418	# reset shape button
	419	self.cbShape.setCurrentIndex(0)
	420	self.cbShape.setEnabled(True)
	421	# reset compute button
	422	self.cmdCompute.setText('Compute')
	423	self.cmdCompute.setEnabled(True)
	424	# TODO reload default data set
	425	self._create_default_sld_data()
	426
	427	finally:
	428	pass
	429
	430	def _create_default_2d_data(self):
	431	"""
	432	Copied from previous version
	433	Create 2D data by default
	434	:warning: This data is never plotted.
	435	"""
	436	self.qmax_x = float(self.txtQxMax.text())
	437	self.npts_x = int(self.txtNoQBins.text())
	438	self.data = Data2D()
	439	self.data.is_data = False
	440	# # Default values
	441	self.data.detector.append(Detector())
	442	index = len(self.data.detector) - 1
	443	self.data.detector[index].distance = 8000 # mm
	444	self.data.source.wavelength = 6 # A
	445	self.data.detector[index].pixel_size.x = 5 # mm
	446	self.data.detector[index].pixel_size.y = 5 # mm
	447	self.data.detector[index].beam_center.x = self.qmax_x
	448	self.data.detector[index].beam_center.y = self.qmax_x
	449	xmax = self.qmax_x
	450	xmin = -xmax
	451	ymax = self.qmax_x
	452	ymin = -ymax
	453	qstep = self.npts_x
	454
	455	x = numpy.linspace(start=xmin, stop=xmax, num=qstep, endpoint=True)
	456	y = numpy.linspace(start=ymin, stop=ymax, num=qstep, endpoint=True)
	457	# use data info instead
	458	new_x = numpy.tile(x, (len(y), 1))
	459	new_y = numpy.tile(y, (len(x), 1))
	460	new_y = new_y.swapaxes(0, 1)
	461	# all data require now in 1d array
	462	qx_data = new_x.flatten()
	463	qy_data = new_y.flatten()
	464	q_data = numpy.sqrt(qx_data * qx_data + qy_data * qy_data)
	465	# set all True (standing for unmasked) as default
	466	mask = numpy.ones(len(qx_data), dtype=bool)
	467	self.data.source = Source()
	468	self.data.data = numpy.ones(len(mask))
	469	self.data.err_data = numpy.ones(len(mask))
	470	self.data.qx_data = qx_data
	471	self.data.qy_data = qy_data
	472	self.data.q_data = q_data
	473	self.data.mask = mask
	474	# store x and y bin centers in q space
	475	self.data.x_bins = x
	476	self.data.y_bins = y
	477	# max and min taking account of the bin sizes
	478	self.data.xmin = xmin
	479	self.data.xmax = xmax
	480	self.data.ymin = ymin
	481	self.data.ymax = ymax
	482
	483	def _create_default_sld_data(self):
	484	"""
	485	Copied from previous version
	486	Making default sld-data
	487	"""
	488	sld_n_default = 6.97e-06 # what is this number??
	489	omfdata = sas_gen.OMFData()
	490	omf2sld = sas_gen.OMF2SLD()
	491	omf2sld.set_data(omfdata, self.default_shape)
	492	self.sld_data = omf2sld.output
	493	self.sld_data.is_data = False
	494	self.sld_data.filename = "Default SLD Profile"
	495	self.sld_data.set_sldn(sld_n_default)
	496
	497	def _create_default_1d_data(self):
	498	"""
	499	Copied from previous version
	500	Create 1D data by default
	501	:warning: This data is never plotted.
	502	residuals.x = data_copy.x[index]
	503	residuals.dy = numpy.ones(len(residuals.y))
	504	residuals.dx = None
	505	residuals.dxl = None
	506	residuals.dxw = None
	507	"""
	508	self.qmax_x = float(self.txtQxMax.text())
	509	self.npts_x = int(self.txtNoQBins.text())
	510	# Default values
	511	xmax = self.qmax_x
	512	xmin = self.qmax_x * _Q1D_MIN
	513	qstep = self.npts_x
	514	x = numpy.linspace(start=xmin, stop=xmax, num=qstep, endpoint=True)
	515	# store x and y bin centers in q space
	516	y = numpy.ones(len(x))
	517	dy = numpy.zeros(len(x))
	518	dx = numpy.zeros(len(x))
	519	self.data = Data1D(x=x, y=y)
	520	self.data.dx = dx
	521	self.data.dy = dy
	522
	523	def onCompute(self):
	524	"""
	525	Copied from previous version
	526	Execute the computation of I(qx, qy)
	527	"""
	528	# Set default data when nothing loaded yet
	529	if self.sld_data is None:
	530	self._create_default_sld_data()
	531	try:
	532	self.model.set_sld_data(self.sld_data)
	533	self.write_new_values_from_gui()
	534	if self.is_avg or self.is_avg is None:
	535	self._create_default_1d_data()
	536	i_out = numpy.zeros(len(self.data.y))
	537	inputs = [self.data.x, [], i_out]
	538	else:
	539	self._create_default_2d_data()
	540	i_out = numpy.zeros(len(self.data.data))
	541	inputs = [self.data.qx_data, self.data.qy_data, i_out]
	542	logging.info("Computation is in progress...")
	543	self.cmdCompute.setText('Wait...')
	544	self.cmdCompute.setEnabled(False)
	545	d = threads.deferToThread(self.complete, inputs, self._update)
	546	# Add deferred callback for call return
	547	d.addCallback(self.plot_1_2d)
[7fb471d]	548	d.addErrback(self.calculateFailed)
[dc5ef15]	549	except:
[b3e8629]	550	log_msg = "{}. stop".format(sys.exc_info()[1])
[dc5ef15]	551	logging.info(log_msg)
	552	return
	553
	554	def _update(self, value):
	555	"""
	556	Copied from previous version
	557	"""
	558	pass
	559
[7fb471d]	560	def calculateFailed(self, reason):
	561	"""
	562	"""
	563	print("Calculate Failed with:\n", reason)
	564	pass
	565
[dc5ef15]	566	def complete(self, input, update=None):
	567	"""
	568	Gen compute complete function
	569	:Param input: input list [qx_data, qy_data, i_out]
	570	"""
	571	out = numpy.empty(0)
	572	for ind in range(len(input[0])):
	573	if self.is_avg:
	574	if ind % 1 == 0 and update is not None:
	575	# update()
	576	percentage = int(100.0 * float(ind) / len(input[0]))
	577	update(percentage)
	578	time.sleep(0.001) # 0.1
	579	inputi = [input[0][ind:ind + 1], [], input[2][ind:ind + 1]]
	580	outi = self.model.run(inputi)
	581	out = numpy.append(out, outi)
	582	else:
	583	if ind % 50 == 0 and update is not None:
	584	percentage = int(100.0 * float(ind) / len(input[0]))
	585	update(percentage)
	586	time.sleep(0.001)
	587	inputi = [input[0][ind:ind + 1], input[1][ind:ind + 1],
	588	input[2][ind:ind + 1]]
	589	outi = self.model.runXY(inputi)
	590	out = numpy.append(out, outi)
	591	self.data_to_plot = out
	592	logging.info('Gen computation completed.')
	593	self.cmdCompute.setText('Compute')
	594	self.cmdCompute.setEnabled(True)
	595	return
	596
	597	def onSaveFile(self):
	598	"""Save data as .sld file"""
	599	path = os.path.dirname(str(self.datafile))
	600	default_name = os.path.join(path, 'sld_file')
	601	kwargs = {
	602	'parent': self,
	603	'directory': default_name,
	604	'filter': 'SLD file (*.sld)',
[4992ff2]	605	'options': QtWidgets.QFileDialog.DontUseNativeDialog}
[dc5ef15]	606	# Query user for filename.
[d6b8a1d]	607	filename_tuple = QtWidgets.QFileDialog.getSaveFileName(**kwargs)
[53c771e]	608	filename = filename_tuple[0]
[dc5ef15]	609	if filename:
	610	try:
[d6b8a1d]	611	_, extension = os.path.splitext(filename)
	612	if not extension:
	613	filename = '.'.join((filename, 'sld'))
	614	sas_gen.SLDReader().write(filename, self.sld_data)
[dc5ef15]	615	except:
	616	raise
	617
	618	def plot3d(self, has_arrow=False):
	619	""" Generate 3D plot in real space with or without arrows """
	620	self.write_new_values_from_gui()
	621	graph_title = " Graph {}: {} 3D SLD Profile".format(self.graph_num,
	622	self.file_name)
	623	if has_arrow:
	624	graph_title += ' - Magnetic Vector as Arrow'
	625
	626	plot3D = Plotter3D(self, graph_title)
	627	plot3D.plot(self.sld_data, has_arrow=has_arrow)
	628	plot3D.show()
	629	self.graph_num += 1
	630
	631	def plot_1_2d(self, d):
	632	""" Generate 1D or 2D plot, called in Compute"""
	633	if self.is_avg or self.is_avg is None:
	634	data = Data1D(x=self.data.x, y=self.data_to_plot)
	635	data.title = "GenSAS {} #{} 1D".format(self.file_name,
	636	int(self.graph_num))
	637	data.xaxis('\\rm{Q_{x}}', '\AA^{-1}')
	638	data.yaxis('\\rm{Intensity}', 'cm^{-1}')
	639	plot1D = Plotter(self)
	640	plot1D.plot(data)
	641	plot1D.show()
	642	self.graph_num += 1
	643	# TODO
[b3e8629]	644	print('TRANSFER OF DATA TO MAIN PANEL TO BE IMPLEMENTED')
[dc5ef15]	645	return plot1D
	646	else:
	647	numpy.nan_to_num(self.data_to_plot)
	648	data = Data2D(image=self.data_to_plot,
	649	qx_data=self.data.qx_data,
	650	qy_data=self.data.qy_data,
	651	q_data=self.data.q_data,
	652	xmin=self.data.xmin, xmax=self.data.ymax,
	653	ymin=self.data.ymin, ymax=self.data.ymax,
	654	err_image=self.data.err_data)
	655	data.title = "GenSAS {} #{} 2D".format(self.file_name,
	656	int(self.graph_num))
	657	plot2D = Plotter2D(self)
	658	plot2D.plot(data)
	659	plot2D.show()
	660	self.graph_num += 1
	661	# TODO
[b3e8629]	662	print('TRANSFER OF DATA TO MAIN PANEL TO BE IMPLEMENTED')
[dc5ef15]	663	return plot2D
	664
	665
	666	class Plotter3DWidget(PlotterBase):
	667	"""
	668	3D Plot widget for use with a QDialog
	669	"""
	670	def __init__(self, parent=None, manager=None):
	671	super(Plotter3DWidget, self).__init__(parent, manager=manager)
	672
	673	@property
	674	def data(self):
	675	return self._data
	676
	677	@data.setter
	678	def data(self, data=None):
	679	""" data setter """
	680	self._data = data
	681
	682	def plot(self, data=None, has_arrow=False):
	683	"""
	684	Plot 3D self._data
	685	"""
[4d1eff2]	686	if not data:
	687	return
[dc5ef15]	688	self.data = data
[4d1eff2]	689	#assert(self._data)
[dc5ef15]	690	# Prepare and show the plot
	691	self.showPlot(data=self.data, has_arrow=has_arrow)
	692
	693	def showPlot(self, data, has_arrow=False):
	694	"""
	695	Render and show the current data
	696	"""
	697	# If we don't have any data, skip.
	698	if data is None:
	699	return
[fef38e8]	700	# This import takes forever - place it here so the main UI starts faster
	701	from mpl_toolkits.mplot3d import Axes3D
[dc5ef15]	702	color_dic = {'H': 'blue', 'D': 'purple', 'N': 'orange',
	703	'O': 'red', 'C': 'green', 'P': 'cyan', 'Other': 'k'}
	704	marker = ','
	705	m_size = 2
	706
	707	pos_x = data.pos_x
	708	pos_y = data.pos_y
	709	pos_z = data.pos_z
	710	sld_mx = data.sld_mx
	711	sld_my = data.sld_my
	712	sld_mz = data.sld_mz
	713	pix_symbol = data.pix_symbol
	714	sld_tot = numpy.fabs(sld_mx) + numpy.fabs(sld_my) + \
	715	numpy.fabs(sld_mz) + numpy.fabs(data.sld_n)
	716	is_nonzero = sld_tot > 0.0
	717	is_zero = sld_tot == 0.0
	718
	719	if data.pix_type == 'atom':
	720	marker = 'o'
	721	m_size = 3.5
	722
	723	self.figure.clear()
	724	self.figure.subplots_adjust(left=0.1, right=.8, bottom=.1)
	725	ax = Axes3D(self.figure)
	726	ax.set_xlabel('x ($\A{}$)'.format(data.pos_unit))
	727	ax.set_ylabel('z ($\A{}$)'.format(data.pos_unit))
	728	ax.set_zlabel('y ($\A{}$)'.format(data.pos_unit))
	729
	730	# I. Plot null points
	731	if is_zero.any():
	732	im = ax.plot(pos_x[is_zero], pos_z[is_zero], pos_y[is_zero],
	733	marker, c="y", alpha=0.5, markeredgecolor='y',
	734	markersize=m_size)
	735	pos_x = pos_x[is_nonzero]
	736	pos_y = pos_y[is_nonzero]
	737	pos_z = pos_z[is_nonzero]
	738	sld_mx = sld_mx[is_nonzero]
	739	sld_my = sld_my[is_nonzero]
	740	sld_mz = sld_mz[is_nonzero]
	741	pix_symbol = data.pix_symbol[is_nonzero]
	742	# II. Plot selective points in color
	743	other_color = numpy.ones(len(pix_symbol), dtype='bool')
[b3e8629]	744	for key in list(color_dic.keys()):
[dc5ef15]	745	chosen_color = pix_symbol == key
	746	if numpy.any(chosen_color):
	747	other_color = other_color & (chosen_color!=True)
	748	color = color_dic[key]
	749	im = ax.plot(pos_x[chosen_color], pos_z[chosen_color],
	750	pos_y[chosen_color], marker, c=color, alpha=0.5,
	751	markeredgecolor=color, markersize=m_size, label=key)
	752	# III. Plot All others
	753	if numpy.any(other_color):
	754	a_name = ''
	755	if data.pix_type == 'atom':
	756	# Get atom names not in the list
	757	a_names = [symb for symb in pix_symbol \
[b3e8629]	758	if symb not in list(color_dic.keys())]
[dc5ef15]	759	a_name = a_names[0]
	760	for name in a_names:
	761	new_name = ", " + name
	762	if a_name.count(name) == 0:
	763	a_name += new_name
	764	# plot in black
	765	im = ax.plot(pos_x[other_color], pos_z[other_color],
	766	pos_y[other_color], marker, c="k", alpha=0.5,
	767	markeredgecolor="k", markersize=m_size, label=a_name)
	768	if data.pix_type == 'atom':
	769	ax.legend(loc='upper left', prop={'size': 10})
	770	# IV. Draws atomic bond with grey lines if any
	771	if data.has_conect:
	772	for ind in range(len(data.line_x)):
	773	im = ax.plot(data.line_x[ind], data.line_z[ind],
	774	data.line_y[ind], '-', lw=0.6, c="grey",
	775	alpha=0.3)
	776	# V. Draws magnetic vectors
	777	if has_arrow and len(pos_x) > 0:
	778	def _draw_arrow(input=None, update=None):
[fef38e8]	779	# import moved here for performance reasons
	780	from sas.qtgui.Plotting.Arrow3D import Arrow3D
[dc5ef15]	781	"""
	782	draw magnetic vectors w/arrow
	783	"""
	784	max_mx = max(numpy.fabs(sld_mx))
	785	max_my = max(numpy.fabs(sld_my))
	786	max_mz = max(numpy.fabs(sld_mz))
	787	max_m = max(max_mx, max_my, max_mz)
	788	try:
	789	max_step = max(data.xstepsize, data.ystepsize, data.zstepsize)
	790	except:
	791	max_step = 0
	792	if max_step <= 0:
	793	max_step = 5
	794	try:
	795	if max_m != 0:
	796	unit_x2 = sld_mx / max_m
	797	unit_y2 = sld_my / max_m
	798	unit_z2 = sld_mz / max_m
	799	# 0.8 is for avoiding the color becomes white=(1,1,1))
	800	color_x = numpy.fabs(unit_x2 * 0.8)
	801	color_y = numpy.fabs(unit_y2 * 0.8)
	802	color_z = numpy.fabs(unit_z2 * 0.8)
	803	x2 = pos_x + unit_x2 * max_step
	804	y2 = pos_y + unit_y2 * max_step
	805	z2 = pos_z + unit_z2 * max_step
	806	x_arrow = numpy.column_stack((pos_x, x2))
	807	y_arrow = numpy.column_stack((pos_y, y2))
	808	z_arrow = numpy.column_stack((pos_z, z2))
	809	colors = numpy.column_stack((color_x, color_y, color_z))
	810	arrows = Arrow3D(self.figure, x_arrow, z_arrow, y_arrow,
	811	colors, mutation_scale=10, lw=1,
	812	arrowstyle="->", alpha=0.5)
	813	ax.add_artist(arrows)
	814	except:
	815	pass
	816	log_msg = "Arrow Drawing completed.\n"
	817	logging.info(log_msg)
	818	log_msg = "Arrow Drawing is in progress..."
	819	logging.info(log_msg)
	820
	821	# Defer the drawing of arrows to another thread
	822	d = threads.deferToThread(_draw_arrow, ax)
	823
	824	self.figure.canvas.resizing = False
	825	self.figure.canvas.draw()
	826
	827
[4992ff2]	828	class Plotter3D(QtWidgets.QDialog, Plotter3DWidget):
[dc5ef15]	829	def __init__(self, parent=None, graph_title=''):
	830	self.graph_title = graph_title
[4992ff2]	831	QtWidgets.QDialog.__init__(self)
[dc5ef15]	832	Plotter3DWidget.__init__(self, manager=parent)
	833	self.setWindowTitle(self.graph_title)
	834

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SasView

source: sasview/src/sas/qtgui/Calculators/GenericScatteringCalculator.py @ aefde77

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