GenericScatteringCalculator.py @ 6b43c58

Last change on this file since 6b43c58 was fef38e8, checked in by Piotr Rozyczko <rozyczko@…>, 7 years ago
Startup time improvements - hiding expensive imports and such
Property mode set to `100644`
File size: 33.5 KB

Rev	Line
[dc5ef15]	1	import sys
	2	import os
	3	import numpy
	4	import logging
	5	import time
	6
	7	from PyQt4 import QtGui
	8	from PyQt4 import QtCore
	9	from twisted.internet import threads
	10
	11	import sas.qtgui.Utilities.GuiUtils as GuiUtils
	12	from sas.qtgui.Utilities.GenericReader import GenReader
	13	from sas.sascalc.dataloader.data_info import Detector
	14	from sas.sascalc.dataloader.data_info import Source
	15	from sas.sascalc.calculator import sas_gen
	16	from sas.qtgui.Plotting.PlotterBase import PlotterBase
	17	from sas.qtgui.Plotting.Plotter2D import Plotter2D
	18	from sas.qtgui.Plotting.Plotter import Plotter
[fef38e8]	19
[dc5ef15]	20	from sas.qtgui.Plotting.PlotterData import Data1D
	21	from sas.qtgui.Plotting.PlotterData import Data2D
	22
	23	# Local UI
	24	from UI.GenericScatteringCalculator import Ui_GenericScatteringCalculator
	25
	26	_Q1D_MIN = 0.001
	27
	28
	29	class GenericScatteringCalculator(QtGui.QDialog, Ui_GenericScatteringCalculator):
	30
	31	trigger_plot_3d = QtCore.pyqtSignal()
	32
	33	def __init__(self, parent=None):
	34	super(GenericScatteringCalculator, self).__init__()
	35	self.setupUi(self)
	36	self.manager = parent
	37	self.communicator = self.manager.communicator()
	38	self.model = sas_gen.GenSAS()
	39	self.omf_reader = sas_gen.OMFReader()
	40	self.sld_reader = sas_gen.SLDReader()
	41	self.pdb_reader = sas_gen.PDBReader()
	42	self.reader = None
	43	self.sld_data = None
	44
	45	self.parameters = []
	46	self.data = None
	47	self.datafile = None
	48	self.file_name = ''
	49	self.ext = None
	50	self.default_shape = str(self.cbShape.currentText())
	51	self.is_avg = False
	52	self.data_to_plot = None
[4d1eff2]	53	self.graph_num = 1 # index for name of graph
[dc5ef15]	54
	55	# combox box
	56	self.cbOptionsCalc.setVisible(False)
	57
	58	# push buttons
	59	self.cmdClose.clicked.connect(self.accept)
	60	self.cmdHelp.clicked.connect(self.onHelp)
	61
	62	self.cmdLoad.clicked.connect(self.loadFile)
	63	self.cmdCompute.clicked.connect(self.onCompute)
	64	self.cmdReset.clicked.connect(self.onReset)
	65	self.cmdSave.clicked.connect(self.onSaveFile)
	66
	67	self.cmdDraw.clicked.connect(lambda: self.plot3d(has_arrow=True))
	68	self.cmdDrawpoints.clicked.connect(lambda: self.plot3d(has_arrow=False))
	69
	70	# validators
	71	# scale, volume and background must be positive
	72	validat_regex_pos = QtCore.QRegExp('^[+]?([.]\d+\|\d+([.]\d+)?)$')
	73	self.txtScale.setValidator(QtGui.QRegExpValidator(validat_regex_pos,
	74	self.txtScale))
	75	self.txtBackground.setValidator(QtGui.QRegExpValidator(
	76	validat_regex_pos, self.txtBackground))
	77	self.txtTotalVolume.setValidator(QtGui.QRegExpValidator(
	78	validat_regex_pos, self.txtTotalVolume))
	79
	80	# fraction of spin up between 0 and 1
	81	validat_regexbetween0_1 = QtCore.QRegExp('^(0(\.\d)\|1(\.0+)?)$')
	82	self.txtUpFracIn.setValidator(
	83	QtGui.QRegExpValidator(validat_regexbetween0_1, self.txtUpFracIn))
	84	self.txtUpFracOut.setValidator(
	85	QtGui.QRegExpValidator(validat_regexbetween0_1, self.txtUpFracOut))
	86
	87	# 0 < Qmax <= 1000
	88	validat_regex_q = QtCore.QRegExp('^1000$\|^[+]?(\d{1,3}([.]\d+)?)$')
	89	self.txtQxMax.setValidator(QtGui.QRegExpValidator(validat_regex_q,
	90	self.txtQxMax))
	91	self.txtQxMax.textChanged.connect(self.check_value)
	92
	93	# 2 <= Qbin <= 1000
	94	self.txtNoQBins.setValidator(QtGui.QRegExpValidator(validat_regex_q,
	95	self.txtNoQBins))
	96	self.txtNoQBins.textChanged.connect(self.check_value)
	97
	98	# plots - 3D in real space
[4d1eff2]	99	self.trigger_plot_3d.connect(lambda: self.plot3d(has_arrow=False))
[dc5ef15]	100
	101	# TODO the option Ellipsoid has not been implemented
	102	self.cbShape.currentIndexChanged.connect(self.selectedshapechange)
	103
[457d961]	104	# New font to display angstrom symbol
	105	new_font = 'font-family: -apple-system, "Helvetica Neue", "Ubuntu";'
	106	self.lblUnitSolventSLD.setStyleSheet(new_font)
	107	self.lblUnitVolume.setStyleSheet(new_font)
	108	self.lbl5.setStyleSheet(new_font)
	109	self.lblUnitMx.setStyleSheet(new_font)
	110	self.lblUnitMy.setStyleSheet(new_font)
	111	self.lblUnitMz.setStyleSheet(new_font)
	112	self.lblUnitNucl.setStyleSheet(new_font)
	113	self.lblUnitx.setStyleSheet(new_font)
	114	self.lblUnity.setStyleSheet(new_font)
	115	self.lblUnitz.setStyleSheet(new_font)
	116
[dc5ef15]	117	def selectedshapechange(self):
	118	"""
	119	TODO Temporary solution to display information about option 'Ellipsoid'
	120	"""
	121	print "The option Ellipsoid has not been implemented yet."
	122	self.communicator.statusBarUpdateSignal.emit(
	123	"The option Ellipsoid has not been implemented yet.")
	124
	125	def loadFile(self):
	126	"""
	127	Open menu to choose the datafile to load
	128	Only extensions .SLD, .PDB, .OMF, .sld, .pdb, .omf
	129	"""
	130	try:
	131	self.datafile = QtGui.QFileDialog.getOpenFileName(
	132	self, "Choose a file", "", "All Gen files (.OMF .omf) ;;"
	133	"SLD files (.SLD .sld);;PDB files (.pdb .PDB);; "
	134	"OMF files (.OMF .omf);; "
	135	"All files (.)")
	136	if self.datafile:
	137	self.default_shape = str(self.cbShape.currentText())
	138	self.file_name = os.path.basename(str(self.datafile))
	139	self.ext = os.path.splitext(str(self.datafile))[1]
	140	if self.ext in self.omf_reader.ext:
	141	loader = self.omf_reader
	142	elif self.ext in self.sld_reader.ext:
	143	loader = self.sld_reader
	144	elif self.ext in self.pdb_reader.ext:
	145	loader = self.pdb_reader
	146	else:
	147	loader = None
	148	# disable some entries depending on type of loaded file
	149	# (according to documentation)
	150	if self.ext.lower() in ['.sld', '.omf', '.pdb']:
	151	self.txtUpFracIn.setEnabled(False)
	152	self.txtUpFracOut.setEnabled(False)
	153	self.txtUpTheta.setEnabled(False)
	154
	155	if self.reader is not None and self.reader.isrunning():
	156	self.reader.stop()
	157	self.cmdLoad.setEnabled(False)
	158	self.cmdLoad.setText('Loading...')
	159	self.communicator.statusBarUpdateSignal.emit(
	160	"Loading File {}".format(os.path.basename(
	161	str(self.datafile))))
	162	self.reader = GenReader(path=str(self.datafile), loader=loader,
	163	completefn=self.complete_loading,
	164	updatefn=self.load_update)
	165	self.reader.queue()
	166	except (RuntimeError, IOError):
	167	log_msg = "Generic SAS Calculator: %s" % sys.exc_value
	168	logging.info(log_msg)
	169	raise
	170	return
	171
	172	def load_update(self):
	173	""" Legacy function used in GenRead """
	174	if self.reader.isrunning():
	175	status_type = "progress"
	176	else:
	177	status_type = "stop"
	178	logging.info(status_type)
	179
	180	def complete_loading(self, data=None):
	181	""" Function used in GenRead"""
	182	self.cbShape.setEnabled(False)
	183	try:
	184	is_pdbdata = False
	185	self.txtData.setText(os.path.basename(str(self.datafile)))
	186	self.is_avg = False
	187	if self.ext in self.omf_reader.ext:
	188	gen = sas_gen.OMF2SLD()
	189	gen.set_data(data)
	190	self.sld_data = gen.get_magsld()
	191	self.check_units()
	192	elif self.ext in self.sld_reader.ext:
	193	self.sld_data = data
	194	elif self.ext in self.pdb_reader.ext:
	195	self.sld_data = data
	196	is_pdbdata = True
	197	# Display combobox of orientation only for pdb data
	198	self.cbOptionsCalc.setVisible(is_pdbdata)
	199	self.update_gui()
	200	except IOError:
	201	log_msg = "Loading Error: " \
	202	"This file format is not supported for GenSAS."
	203	logging.info(log_msg)
	204	raise
	205	except ValueError:
	206	log_msg = "Could not find any data"
	207	logging.info(log_msg)
	208	raise
	209	logging.info("Load Complete")
	210	self.cmdLoad.setEnabled(True)
	211	self.cmdLoad.setText('Load')
	212	self.trigger_plot_3d.emit()
	213
	214	def check_units(self):
	215	"""
	216	Check if the units from the OMF file correspond to the default ones
	217	displayed on the interface.
	218	If not, modify the GUI with the correct unit
	219	"""
	220	# TODO: adopt the convention of font and symbol for the updated values
	221	if sas_gen.OMFData().valueunit != 'A^(-2)':
	222	value_unit = sas_gen.OMFData().valueunit
	223	self.lbl_unitMx.setText(value_unit)
	224	self.lbl_unitMy.setText(value_unit)
	225	self.lbl_unitMz.setText(value_unit)
	226	self.lbl_unitNucl.setText(value_unit)
	227	if sas_gen.OMFData().meshunit != 'A':
	228	mesh_unit = sas_gen.OMFData().meshunit
	229	self.lbl_unitx.setText(mesh_unit)
	230	self.lbl_unity.setText(mesh_unit)
	231	self.lbl_unitz.setText(mesh_unit)
	232	self.lbl_unitVolume.setText(mesh_unit+"^3")
	233
	234	def check_value(self):
	235	"""Check range of text edits for QMax and Number of Qbins """
	236	text_edit = self.sender()
	237	text_edit.setStyleSheet(
	238	QtCore.QString.fromUtf8('background-color: rgb(255, 255, 255);'))
	239	if text_edit.text():
	240	value = float(str(text_edit.text()))
	241	if text_edit == self.txtQxMax:
	242	if value <= 0 or value > 1000:
	243	text_edit.setStyleSheet(QtCore.QString.fromUtf8(
	244	'background-color: rgb(255, 182, 193);'))
	245	else:
	246	text_edit.setStyleSheet(QtCore.QString.fromUtf8(
	247	'background-color: rgb(255, 255, 255);'))
	248	elif text_edit == self.txtNoQBins:
	249	if value < 2 or value > 1000:
	250	self.txtNoQBins.setStyleSheet(QtCore.QString.fromUtf8(
	251	'background-color: rgb(255, 182, 193);'))
	252	else:
	253	self.txtNoQBins.setStyleSheet(QtCore.QString.fromUtf8(
	254	'background-color: rgb(255, 255, 255);'))
	255
	256	def update_gui(self):
	257	""" Update the interface with values from loaded data """
	258	self.model.set_is_avg(self.is_avg)
	259	self.model.set_sld_data(self.sld_data)
	260	self.model.params['total_volume'] = len(self.sld_data.sld_n)*self.sld_data.vol_pix[0]
	261
	262	# add condition for activation of save button
	263	self.cmdSave.setEnabled(True)
	264
	265	# activation of 3D plots' buttons (with and without arrows)
	266	self.cmdDraw.setEnabled(self.sld_data is not None)
	267	self.cmdDrawpoints.setEnabled(self.sld_data is not None)
	268
	269	self.txtScale.setText(str(self.model.params['scale']))
	270	self.txtBackground.setText(str(self.model.params['background']))
	271	self.txtSolventSLD.setText(str(self.model.params['solvent_SLD']))
	272
	273	# Volume to write to interface: npts x volume of first pixel
	274	self.txtTotalVolume.setText(str(len(self.sld_data.sld_n)*self.sld_data.vol_pix[0]))
	275
	276	self.txtUpFracIn.setText(str(self.model.params['Up_frac_in']))
	277	self.txtUpFracOut.setText(str(self.model.params['Up_frac_out']))
	278	self.txtUpTheta.setText(str(self.model.params['Up_theta']))
	279
	280	self.txtNoPixels.setText(str(len(self.sld_data.sld_n)))
	281	self.txtNoPixels.setEnabled(False)
	282
	283	list_parameters = ['sld_mx', 'sld_my', 'sld_mz', 'sld_n', 'xnodes',
	284	'ynodes', 'znodes', 'xstepsize', 'ystepsize',
	285	'zstepsize']
	286	list_gui_button = [self.txtMx, self.txtMy, self.txtMz, self.txtNucl,
	287	self.txtXnodes, self.txtYnodes, self.txtZnodes,
	288	self.txtXstepsize, self.txtYstepsize,
	289	self.txtZstepsize]
	290
	291	# Fill right hand side of GUI
	292	for indx, item in enumerate(list_parameters):
	293	if getattr(self.sld_data, item) is None:
	294	list_gui_button[indx].setText('NaN')
	295	else:
	296	value = getattr(self.sld_data, item)
	297	if isinstance(value, numpy.ndarray):
	298	item_for_gui = str(GuiUtils.formatNumber(numpy.average(value), True))
	299	else:
	300	item_for_gui = str(GuiUtils.formatNumber(value, True))
	301	list_gui_button[indx].setText(item_for_gui)
	302
	303	# Enable / disable editing of right hand side of GUI
	304	for indx, item in enumerate(list_parameters):
	305	if indx < 4:
	306	# this condition only applies to Mx,y,z and Nucl
	307	value = getattr(self.sld_data, item)
	308	enable = self.sld_data.pix_type == 'pixel' \
	309	and numpy.min(value) == numpy.max(value)
	310	else:
	311	enable = not self.sld_data.is_data
	312	list_gui_button[indx].setEnabled(enable)
	313
	314	def write_new_values_from_gui(self):
	315	"""
	316	update parameters using modified inputs from GUI
	317	used before computing
	318	"""
	319	if self.txtScale.isModified():
	320	self.model.params['scale'] = float(self.txtScale.text())
	321
	322	if self.txtBackground.isModified():
	323	self.model.params['background'] = float(self.txtBackground.text())
	324
	325	if self.txtSolventSLD.isModified():
	326	self.model.params['solvent_SLD'] = float(self.txtSolventSLD.text())
	327
	328	# Different condition for total volume to get correct volume after
	329	# applying set_sld_data in compute
	330	if self.txtTotalVolume.isModified() \
	331	or self.model.params['total_volume'] != float(self.txtTotalVolume.text()):
	332	self.model.params['total_volume'] = float(self.txtTotalVolume.text())
	333
	334	if self.txtUpFracIn.isModified():
	335	self.model.params['Up_frac_in'] = float(self.txtUpFracIn.text())
	336
	337	if self.txtUpFracOut.isModified():
	338	self.model.params['Up_frac_out'] = float(self.txtUpFracOut.text())
	339
	340	if self.txtUpTheta.isModified():
	341	self.model.params['Up_theta'] = float(self.txtUpTheta.text())
	342
	343	if self.txtMx.isModified():
	344	self.sld_data.sld_mx = float(self.txtMx.text())*\
	345	numpy.ones(len(self.sld_data.sld_mx))
	346
	347	if self.txtMy.isModified():
	348	self.sld_data.sld_my = float(self.txtMy.text())*\
	349	numpy.ones(len(self.sld_data.sld_my))
	350
	351	if self.txtMz.isModified():
	352	self.sld_data.sld_mz = float(self.txtMz.text())*\
	353	numpy.ones(len(self.sld_data.sld_mz))
	354
	355	if self.txtNucl.isModified():
	356	self.sld_data.sld_n = float(self.txtNucl.text())*\
	357	numpy.ones(len(self.sld_data.sld_n))
	358
	359	if self.txtXnodes.isModified():
	360	self.sld_data.xnodes = int(self.txtXnodes.text())
	361
	362	if self.txtYnodes.isModified():
	363	self.sld_data.ynodes = int(self.txtYnodes.text())
	364
	365	if self.txtZnodes.isModified():
	366	self.sld_data.znodes = int(self.txtZnodes.text())
	367
	368	if self.txtXstepsize.isModified():
	369	self.sld_data.xstepsize = float(self.txtXstepsize.text())
	370
	371	if self.txtYstepsize.isModified():
	372	self.sld_data.ystepsize = float(self.txtYstepsize.text())
	373
	374	if self.txtZstepsize.isModified():
	375	self.sld_data.zstepsize = float(self.txtZstepsize.text())
	376
	377	if self.cbOptionsCalc.isVisible():
	378	self.is_avg = (self.cbOptionsCalc.currentIndex() == 1)
	379
	380	def onHelp(self):
	381	"""
	382	Bring up the Generic Scattering calculator Documentation whenever
	383	the HELP button is clicked.
	384	Calls Documentation Window with the path of the location within the
	385	documentation tree (after /doc/ ....".
	386	"""
	387	try:
[b0c5e8c]	388	location = GuiUtils.HELP_DIRECTORY_LOCATION + \
[dc5ef15]	389	"/user/sasgui/perspectives/calculator/sas_calculator_help.html"
	390	self.manager._helpView.load(QtCore.QUrl(location))
	391	self.manager._helpView.show()
	392	except AttributeError:
	393	# No manager defined - testing and standalone runs
	394	pass
	395
	396	def onReset(self):
	397	""" Reset the inputs of textEdit to default values """
	398	try:
	399	# reset values in textedits
	400	self.txtUpFracIn.setText("1.0")
	401	self.txtUpFracOut.setText("1.0")
	402	self.txtUpTheta.setText("0.0")
	403	self.txtBackground.setText("0.0")
	404	self.txtScale.setText("1.0")
	405	self.txtSolventSLD.setText("0.0")
	406	self.txtTotalVolume.setText("216000.0")
	407	self.txtNoQBins.setText("50")
	408	self.txtQxMax.setText("0.3")
	409	self.txtNoPixels.setText("1000")
	410	self.txtMx.setText("0")
	411	self.txtMy.setText("0")
	412	self.txtMz.setText("0")
	413	self.txtNucl.setText("6.97e-06")
	414	self.txtXnodes.setText("10")
	415	self.txtYnodes.setText("10")
	416	self.txtZnodes.setText("10")
	417	self.txtXstepsize.setText("6")
	418	self.txtYstepsize.setText("6")
	419	self.txtZstepsize.setText("6")
	420	# reset Load button and textedit
	421	self.txtData.setText('Default SLD Profile')
	422	self.cmdLoad.setEnabled(True)
	423	self.cmdLoad.setText('Load')
	424	# reset option for calculation
	425	self.cbOptionsCalc.setCurrentIndex(0)
	426	self.cbOptionsCalc.setVisible(False)
	427	# reset shape button
	428	self.cbShape.setCurrentIndex(0)
	429	self.cbShape.setEnabled(True)
	430	# reset compute button
	431	self.cmdCompute.setText('Compute')
	432	self.cmdCompute.setEnabled(True)
	433	# TODO reload default data set
	434	self._create_default_sld_data()
	435
	436	finally:
	437	pass
	438
	439	def _create_default_2d_data(self):
	440	"""
	441	Copied from previous version
	442	Create 2D data by default
	443	:warning: This data is never plotted.
	444	"""
	445	self.qmax_x = float(self.txtQxMax.text())
	446	self.npts_x = int(self.txtNoQBins.text())
	447	self.data = Data2D()
	448	self.data.is_data = False
	449	# # Default values
	450	self.data.detector.append(Detector())
	451	index = len(self.data.detector) - 1
	452	self.data.detector[index].distance = 8000 # mm
	453	self.data.source.wavelength = 6 # A
	454	self.data.detector[index].pixel_size.x = 5 # mm
	455	self.data.detector[index].pixel_size.y = 5 # mm
	456	self.data.detector[index].beam_center.x = self.qmax_x
	457	self.data.detector[index].beam_center.y = self.qmax_x
	458	xmax = self.qmax_x
	459	xmin = -xmax
	460	ymax = self.qmax_x
	461	ymin = -ymax
	462	qstep = self.npts_x
	463
	464	x = numpy.linspace(start=xmin, stop=xmax, num=qstep, endpoint=True)
	465	y = numpy.linspace(start=ymin, stop=ymax, num=qstep, endpoint=True)
	466	# use data info instead
	467	new_x = numpy.tile(x, (len(y), 1))
	468	new_y = numpy.tile(y, (len(x), 1))
	469	new_y = new_y.swapaxes(0, 1)
	470	# all data require now in 1d array
	471	qx_data = new_x.flatten()
	472	qy_data = new_y.flatten()
	473	q_data = numpy.sqrt(qx_data * qx_data + qy_data * qy_data)
	474	# set all True (standing for unmasked) as default
	475	mask = numpy.ones(len(qx_data), dtype=bool)
	476	self.data.source = Source()
	477	self.data.data = numpy.ones(len(mask))
	478	self.data.err_data = numpy.ones(len(mask))
	479	self.data.qx_data = qx_data
	480	self.data.qy_data = qy_data
	481	self.data.q_data = q_data
	482	self.data.mask = mask
	483	# store x and y bin centers in q space
	484	self.data.x_bins = x
	485	self.data.y_bins = y
	486	# max and min taking account of the bin sizes
	487	self.data.xmin = xmin
	488	self.data.xmax = xmax
	489	self.data.ymin = ymin
	490	self.data.ymax = ymax
	491
	492	def _create_default_sld_data(self):
	493	"""
	494	Copied from previous version
	495	Making default sld-data
	496	"""
	497	sld_n_default = 6.97e-06 # what is this number??
	498	omfdata = sas_gen.OMFData()
	499	omf2sld = sas_gen.OMF2SLD()
	500	omf2sld.set_data(omfdata, self.default_shape)
	501	self.sld_data = omf2sld.output
	502	self.sld_data.is_data = False
	503	self.sld_data.filename = "Default SLD Profile"
	504	self.sld_data.set_sldn(sld_n_default)
	505
	506	def _create_default_1d_data(self):
	507	"""
	508	Copied from previous version
	509	Create 1D data by default
	510	:warning: This data is never plotted.
	511	residuals.x = data_copy.x[index]
	512	residuals.dy = numpy.ones(len(residuals.y))
	513	residuals.dx = None
	514	residuals.dxl = None
	515	residuals.dxw = None
	516	"""
	517	self.qmax_x = float(self.txtQxMax.text())
	518	self.npts_x = int(self.txtNoQBins.text())
	519	# Default values
	520	xmax = self.qmax_x
	521	xmin = self.qmax_x * _Q1D_MIN
	522	qstep = self.npts_x
	523	x = numpy.linspace(start=xmin, stop=xmax, num=qstep, endpoint=True)
	524	# store x and y bin centers in q space
	525	y = numpy.ones(len(x))
	526	dy = numpy.zeros(len(x))
	527	dx = numpy.zeros(len(x))
	528	self.data = Data1D(x=x, y=y)
	529	self.data.dx = dx
	530	self.data.dy = dy
	531
	532	def onCompute(self):
	533	"""
	534	Copied from previous version
	535	Execute the computation of I(qx, qy)
	536	"""
	537	# Set default data when nothing loaded yet
	538	if self.sld_data is None:
	539	self._create_default_sld_data()
	540	try:
	541	self.model.set_sld_data(self.sld_data)
	542	self.write_new_values_from_gui()
	543	if self.is_avg or self.is_avg is None:
	544	self._create_default_1d_data()
	545	i_out = numpy.zeros(len(self.data.y))
	546	inputs = [self.data.x, [], i_out]
	547	else:
	548	self._create_default_2d_data()
	549	i_out = numpy.zeros(len(self.data.data))
	550	inputs = [self.data.qx_data, self.data.qy_data, i_out]
	551	logging.info("Computation is in progress...")
	552	self.cmdCompute.setText('Wait...')
	553	self.cmdCompute.setEnabled(False)
	554	d = threads.deferToThread(self.complete, inputs, self._update)
	555	# Add deferred callback for call return
	556	d.addCallback(self.plot_1_2d)
	557	except:
	558	log_msg = "{}. stop".format(sys.exc_value)
	559	logging.info(log_msg)
	560	return
	561
	562	def _update(self, value):
	563	"""
	564	Copied from previous version
	565	"""
	566	pass
	567
	568	def complete(self, input, update=None):
	569	"""
	570	Gen compute complete function
	571	:Param input: input list [qx_data, qy_data, i_out]
	572	"""
	573	out = numpy.empty(0)
	574	for ind in range(len(input[0])):
	575	if self.is_avg:
	576	if ind % 1 == 0 and update is not None:
	577	# update()
	578	percentage = int(100.0 * float(ind) / len(input[0]))
	579	update(percentage)
	580	time.sleep(0.001) # 0.1
	581	inputi = [input[0][ind:ind + 1], [], input[2][ind:ind + 1]]
	582	outi = self.model.run(inputi)
	583	out = numpy.append(out, outi)
	584	else:
	585	if ind % 50 == 0 and update is not None:
	586	percentage = int(100.0 * float(ind) / len(input[0]))
	587	update(percentage)
	588	time.sleep(0.001)
	589	inputi = [input[0][ind:ind + 1], input[1][ind:ind + 1],
	590	input[2][ind:ind + 1]]
	591	outi = self.model.runXY(inputi)
	592	out = numpy.append(out, outi)
	593	self.data_to_plot = out
	594	logging.info('Gen computation completed.')
	595	self.cmdCompute.setText('Compute')
	596	self.cmdCompute.setEnabled(True)
	597	return
	598
	599	def onSaveFile(self):
	600	"""Save data as .sld file"""
	601	path = os.path.dirname(str(self.datafile))
	602	default_name = os.path.join(path, 'sld_file')
	603	kwargs = {
	604	'parent': self,
	605	'directory': default_name,
	606	'filter': 'SLD file (*.sld)',
	607	'options': QtGui.QFileDialog.DontUseNativeDialog}
	608	# Query user for filename.
	609	filename = str(QtGui.QFileDialog.getSaveFileName(**kwargs))
	610	if filename:
	611	try:
	612	if os.path.splitext(filename)[1].lower() == '.sld':
	613	sas_gen.SLDReader().write(filename, self.sld_data)
	614	else:
	615	sas_gen.SLDReader().write('.'.join((filename, 'sld')),
	616	self.sld_data)
	617	except:
	618	raise
	619
	620	def plot3d(self, has_arrow=False):
	621	""" Generate 3D plot in real space with or without arrows """
	622	self.write_new_values_from_gui()
	623	graph_title = " Graph {}: {} 3D SLD Profile".format(self.graph_num,
	624	self.file_name)
	625	if has_arrow:
	626	graph_title += ' - Magnetic Vector as Arrow'
	627
	628	plot3D = Plotter3D(self, graph_title)
	629	plot3D.plot(self.sld_data, has_arrow=has_arrow)
	630	plot3D.show()
	631	self.graph_num += 1
	632
	633	def plot_1_2d(self, d):
	634	""" Generate 1D or 2D plot, called in Compute"""
	635	if self.is_avg or self.is_avg is None:
	636	data = Data1D(x=self.data.x, y=self.data_to_plot)
	637	data.title = "GenSAS {} #{} 1D".format(self.file_name,
	638	int(self.graph_num))
	639	data.xaxis('\\rm{Q_{x}}', '\AA^{-1}')
	640	data.yaxis('\\rm{Intensity}', 'cm^{-1}')
	641	plot1D = Plotter(self)
	642	plot1D.plot(data)
	643	plot1D.show()
	644	self.graph_num += 1
	645	# TODO
	646	print 'TRANSFER OF DATA TO MAIN PANEL TO BE IMPLEMENTED'
	647	return plot1D
	648	else:
	649	numpy.nan_to_num(self.data_to_plot)
	650	data = Data2D(image=self.data_to_plot,
	651	qx_data=self.data.qx_data,
	652	qy_data=self.data.qy_data,
	653	q_data=self.data.q_data,
	654	xmin=self.data.xmin, xmax=self.data.ymax,
	655	ymin=self.data.ymin, ymax=self.data.ymax,
	656	err_image=self.data.err_data)
	657	data.title = "GenSAS {} #{} 2D".format(self.file_name,
	658	int(self.graph_num))
	659	plot2D = Plotter2D(self)
	660	plot2D.plot(data)
	661	plot2D.show()
	662	self.graph_num += 1
	663	# TODO
	664	print 'TRANSFER OF DATA TO MAIN PANEL TO BE IMPLEMENTED'
	665	return plot2D
	666
	667
	668	class Plotter3DWidget(PlotterBase):
	669	"""
	670	3D Plot widget for use with a QDialog
	671	"""
	672	def __init__(self, parent=None, manager=None):
	673	super(Plotter3DWidget, self).__init__(parent, manager=manager)
	674
	675	@property
	676	def data(self):
	677	return self._data
	678
	679	@data.setter
	680	def data(self, data=None):
	681	""" data setter """
	682	self._data = data
	683
	684	def plot(self, data=None, has_arrow=False):
	685	"""
	686	Plot 3D self._data
	687	"""
[4d1eff2]	688	if not data:
	689	return
[dc5ef15]	690	self.data = data
[4d1eff2]	691	#assert(self._data)
[dc5ef15]	692	# Prepare and show the plot
	693	self.showPlot(data=self.data, has_arrow=has_arrow)
	694
	695	def showPlot(self, data, has_arrow=False):
	696	"""
	697	Render and show the current data
	698	"""
	699	# If we don't have any data, skip.
	700	if data is None:
	701	return
[fef38e8]	702	# This import takes forever - place it here so the main UI starts faster
	703	from mpl_toolkits.mplot3d import Axes3D
[dc5ef15]	704	color_dic = {'H': 'blue', 'D': 'purple', 'N': 'orange',
	705	'O': 'red', 'C': 'green', 'P': 'cyan', 'Other': 'k'}
	706	marker = ','
	707	m_size = 2
	708
	709	pos_x = data.pos_x
	710	pos_y = data.pos_y
	711	pos_z = data.pos_z
	712	sld_mx = data.sld_mx
	713	sld_my = data.sld_my
	714	sld_mz = data.sld_mz
	715	pix_symbol = data.pix_symbol
	716	sld_tot = numpy.fabs(sld_mx) + numpy.fabs(sld_my) + \
	717	numpy.fabs(sld_mz) + numpy.fabs(data.sld_n)
	718	is_nonzero = sld_tot > 0.0
	719	is_zero = sld_tot == 0.0
	720
	721	if data.pix_type == 'atom':
	722	marker = 'o'
	723	m_size = 3.5
	724
	725	self.figure.clear()
	726	self.figure.subplots_adjust(left=0.1, right=.8, bottom=.1)
	727	ax = Axes3D(self.figure)
	728	ax.set_xlabel('x ($\A{}$)'.format(data.pos_unit))
	729	ax.set_ylabel('z ($\A{}$)'.format(data.pos_unit))
	730	ax.set_zlabel('y ($\A{}$)'.format(data.pos_unit))
	731
	732	# I. Plot null points
	733	if is_zero.any():
	734	im = ax.plot(pos_x[is_zero], pos_z[is_zero], pos_y[is_zero],
	735	marker, c="y", alpha=0.5, markeredgecolor='y',
	736	markersize=m_size)
	737	pos_x = pos_x[is_nonzero]
	738	pos_y = pos_y[is_nonzero]
	739	pos_z = pos_z[is_nonzero]
	740	sld_mx = sld_mx[is_nonzero]
	741	sld_my = sld_my[is_nonzero]
	742	sld_mz = sld_mz[is_nonzero]
	743	pix_symbol = data.pix_symbol[is_nonzero]
	744	# II. Plot selective points in color
	745	other_color = numpy.ones(len(pix_symbol), dtype='bool')
	746	for key in color_dic.keys():
	747	chosen_color = pix_symbol == key
	748	if numpy.any(chosen_color):
	749	other_color = other_color & (chosen_color!=True)
	750	color = color_dic[key]
	751	im = ax.plot(pos_x[chosen_color], pos_z[chosen_color],
	752	pos_y[chosen_color], marker, c=color, alpha=0.5,
	753	markeredgecolor=color, markersize=m_size, label=key)
	754	# III. Plot All others
	755	if numpy.any(other_color):
	756	a_name = ''
	757	if data.pix_type == 'atom':
	758	# Get atom names not in the list
	759	a_names = [symb for symb in pix_symbol \
	760	if symb not in color_dic.keys()]
	761	a_name = a_names[0]
	762	for name in a_names:
	763	new_name = ", " + name
	764	if a_name.count(name) == 0:
	765	a_name += new_name
	766	# plot in black
	767	im = ax.plot(pos_x[other_color], pos_z[other_color],
	768	pos_y[other_color], marker, c="k", alpha=0.5,
	769	markeredgecolor="k", markersize=m_size, label=a_name)
	770	if data.pix_type == 'atom':
	771	ax.legend(loc='upper left', prop={'size': 10})
	772	# IV. Draws atomic bond with grey lines if any
	773	if data.has_conect:
	774	for ind in range(len(data.line_x)):
	775	im = ax.plot(data.line_x[ind], data.line_z[ind],
	776	data.line_y[ind], '-', lw=0.6, c="grey",
	777	alpha=0.3)
	778	# V. Draws magnetic vectors
	779	if has_arrow and len(pos_x) > 0:
	780	def _draw_arrow(input=None, update=None):
[fef38e8]	781	# import moved here for performance reasons
	782	from sas.qtgui.Plotting.Arrow3D import Arrow3D
[dc5ef15]	783	"""
	784	draw magnetic vectors w/arrow
	785	"""
	786	max_mx = max(numpy.fabs(sld_mx))
	787	max_my = max(numpy.fabs(sld_my))
	788	max_mz = max(numpy.fabs(sld_mz))
	789	max_m = max(max_mx, max_my, max_mz)
	790	try:
	791	max_step = max(data.xstepsize, data.ystepsize, data.zstepsize)
	792	except:
	793	max_step = 0
	794	if max_step <= 0:
	795	max_step = 5
	796	try:
	797	if max_m != 0:
	798	unit_x2 = sld_mx / max_m
	799	unit_y2 = sld_my / max_m
	800	unit_z2 = sld_mz / max_m
	801	# 0.8 is for avoiding the color becomes white=(1,1,1))
	802	color_x = numpy.fabs(unit_x2 * 0.8)
	803	color_y = numpy.fabs(unit_y2 * 0.8)
	804	color_z = numpy.fabs(unit_z2 * 0.8)
	805	x2 = pos_x + unit_x2 * max_step
	806	y2 = pos_y + unit_y2 * max_step
	807	z2 = pos_z + unit_z2 * max_step
	808	x_arrow = numpy.column_stack((pos_x, x2))
	809	y_arrow = numpy.column_stack((pos_y, y2))
	810	z_arrow = numpy.column_stack((pos_z, z2))
	811	colors = numpy.column_stack((color_x, color_y, color_z))
	812	arrows = Arrow3D(self.figure, x_arrow, z_arrow, y_arrow,
	813	colors, mutation_scale=10, lw=1,
	814	arrowstyle="->", alpha=0.5)
	815	ax.add_artist(arrows)
	816	except:
	817	pass
	818	log_msg = "Arrow Drawing completed.\n"
	819	logging.info(log_msg)
	820	log_msg = "Arrow Drawing is in progress..."
	821	logging.info(log_msg)
	822
	823	# Defer the drawing of arrows to another thread
	824	d = threads.deferToThread(_draw_arrow, ax)
	825
	826	self.figure.canvas.resizing = False
	827	self.figure.canvas.draw()
	828
	829
	830	class Plotter3D(QtGui.QDialog, Plotter3DWidget):
	831	def __init__(self, parent=None, graph_title=''):
	832	self.graph_title = graph_title
	833	QtGui.QDialog.__init__(self)
	834	Plotter3DWidget.__init__(self, manager=parent)
	835	self.setWindowTitle(self.graph_title)
	836

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SasView

source: sasview/src/sas/qtgui/Calculators/GenericScatteringCalculator.py @ 6b43c58

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