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refl_gui.py
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refl_gui.py
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import refl_window
import refl_save
import refl_choose_col
import refl_options
import csv
import string
import os
import re
from operator import itemgetter
import itertools
from PyQt4 import QtCore, QtGui
from mantid.simpleapi import *
from isis_reflectometry.quick import *
from isis_reflectometry.convert_to_wavelength import ConvertToWavelength
from isis_reflectometry import load_live_runs
from isis_reflectometry.combineMulti import *
from mantid.api import Workspace, WorkspaceGroup, CatalogManager, AlgorithmManager
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
_fromUtf8 = lambda s: s
canMantidPlot = True
try:
from mantidplot import *
except ImportError:
canMantidPlot = False
class ReflGui(QtGui.QMainWindow, refl_window.Ui_windowRefl):
def __init__(self):
"""
Initialise the interface
"""
super(QtGui.QMainWindow, self).__init__()
self.setupUi(self)
self.loading = False
self.clip = QtGui.QApplication.clipboard()
self.shown_cols = {}
self.mod_flag = False
self.run_cols = [0,5,10]
self.angle_cols = [1,6,11]
self.scale_col = 16
self.stitch_col = 17
self.plot_col = 18
self._last_trans = ""
self.__icat_file_map = None
self.__instrumentRuns = None
self.__icat_download = False
# Q Settings
self.__generic_settings = "Mantid/ISISReflGui"
self.__live_data_settings = "Mantid/ISISReflGui/LiveData"
self.__search_settings = "Mantid/ISISReflGui/Search"
self.__column_settings = "Mantid/ISISReflGui/Columns"
self.__icat_download_key = "icat_download"
self.__ads_use_key = "AlgUse"
self.__live_data_frequency_key = "frequency"
self.__live_data_method_key = "method"
#Setup instrument options with defaults assigned.
self.instrument_list = ['INTER', 'SURF', 'CRISP', 'POLREF']
self.polarisation_instruments = ['CRISP', 'POLREF']
self.polarisation_options = {'None' : PolarisationCorrection.NONE, '1-PNR' : PolarisationCorrection.PNR, '2-PA' : PolarisationCorrection.PA }
#Set the live data settings, use default if none have been set before
settings = QtCore.QSettings()
settings.beginGroup(self.__live_data_settings)
self.live_method = settings.value(self.__live_data_method_key, "", type=str)
self.live_freq = settings.value(self.__live_data_frequency_key, 0, type=float)
if not (self.live_freq):
logger.information("No settings were found for Update frequency of loading live data, Loading default of 60 seconds")
self.live_freq = float(60)
settings.setValue(self.__live_data_frequency_key, self.live_freq)
if not (self.live_method):
logger.information("No settings were found for Accumulation Method of loading live data, Loading default of \"Add\"")
self.live_method = "Add"
settings.setValue(self.__live_data_method_key, self.live_method)
settings.endGroup()
settings.beginGroup(self.__generic_settings)
self.alg_use = settings.value(self.__ads_use_key, False, type=bool)
self.__icat_download = settings.value(self.__icat_download_key, False, type=bool)
settings.setValue(self.__ads_use_key, self.alg_use)
settings.setValue(self.__icat_download_key, self.__icat_download)
settings.endGroup()
del settings
def __del__(self):
"""
Save the contents of the table if the modified flag was still set
"""
if self.mod_flag:
self._save(true)
def _save_check(self):
"""
Show a standard message box asking if the user wants to save, or discard their changes or cancel back to the interface
"""
msgBox = QtGui.QMessageBox()
msgBox.setText("The table has been modified. Do you want to save your changes?")
msgBox.setStandardButtons(QtGui.QMessageBox.Save | QtGui.QMessageBox.Discard | QtGui.QMessageBox.Cancel)
msgBox.setIcon(QtGui.QMessageBox.Question)
msgBox.setDefaultButton(QtGui.QMessageBox.Save)
msgBox.setEscapeButton(QtGui.QMessageBox.Cancel)
ret = msgBox.exec_()
saved = None
if ret == QtGui.QMessageBox.Save:
saved = self._save()
return ret, saved
def closeEvent(self, event):
"""
Close the window. but check if the user wants to save
"""
self.buttonProcess.setFocus()
if self.mod_flag:
event.ignore()
ret, saved = self._save_check()
if ret == QtGui.QMessageBox.Save:
if saved:
event.accept()
elif ret == QtGui.QMessageBox.Discard:
self.mod_flag = False
event.accept()
def _instrument_selected(self, instrument):
"""
Change the default instrument to the selected one
"""
config['default.instrument'] = self.instrument_list[instrument]
logger.notice( "Instrument is now: " + str(config['default.instrument']))
self.textRB.clear()
self._populate_runs_list()
self.current_instrument = self.instrument_list[instrument]
self.comboPolarCorrect.setEnabled(self.current_instrument in self.polarisation_instruments) # Enable as appropriate
self.comboPolarCorrect.setCurrentIndex(self.comboPolarCorrect.findText('None')) # Reset to None
def _table_modified(self, row, column):
"""
sets the modified flag when the table is altered
"""
#Sometimes users enter leading or trailing whitespace into a cell.
#Let's remove it for them automatically.
item = self.tableMain.item(row, column)
item.setData(0, str.strip(str(item.data(0))))
if not self.loading:
self.mod_flag = True
plotbutton = self.tableMain.cellWidget(row, self.plot_col).children()[1]
self.__reset_plot_button(plotbutton)
def _plot_row(self):
"""
handler for the plot buttons
"""
plotbutton = self.sender()
self._plot(plotbutton)
def _polar_corr_selected(self):
"""
Event handler for polarisation correction selection.
"""
if self.current_instrument in self.polarisation_instruments:
chosen_method = self.comboPolarCorrect.currentText()
self.current_polarisation_method = self.polarisation_options[chosen_method]
else:
logger.notice("Polarisation correction is not supported on " + str(self.current_instrument))
def setup_layout(self):
"""
Do further setup layout that couldn't be done in the designer
"""
self.comboInstrument.addItems(self.instrument_list)
current_instrument = config['default.instrument'].upper()
if current_instrument in self.instrument_list:
self.comboInstrument.setCurrentIndex(self.instrument_list.index(current_instrument))
else:
self.comboInstrument.setCurrentIndex(0)
config['default.instrument'] = 'INTER'
self.current_instrument = config['default.instrument'].upper()
#Setup polarisation options with default assigned
self.comboPolarCorrect.clear()
self.comboPolarCorrect.addItems(self.polarisation_options.keys())
self.comboPolarCorrect.setCurrentIndex(self.comboPolarCorrect.findText('None'))
self.current_polarisation_method = self.polarisation_options['None']
self.comboPolarCorrect.setEnabled(self.current_instrument in self.polarisation_instruments)
self.splitterList.setSizes([200, 800])
self.labelStatus = QtGui.QLabel("Ready")
self.statusMain.addWidget(self.labelStatus)
self._initialise_table()
self._populate_runs_list()
self._connect_slots()
return True
def _reset_table(self):
"""
Reset the plot buttons and stitch checkboxes back to thier defualt state
"""
#switches from current to true, to false to make sure stateChanged fires
self.checkTickAll.setCheckState(2)
self.checkTickAll.setCheckState(0)
for row in range(self.tableMain.rowCount()):
plotbutton = self.tableMain.cellWidget(row, self.plot_col).children()[1]
self.__reset_plot_button(plotbutton)
def __reset_plot_button(self, plotbutton):
"""
Reset the provided plot button to ti's default state: disabled and with no cache
"""
plotbutton.setDisabled(True)
plotbutton.setProperty('runno', None)
plotbutton.setProperty('overlapLow', None)
plotbutton.setProperty('overlapHigh', None)
plotbutton.setProperty('wksp', None)
def _initialise_table(self):
"""
Initialise the table. Clearing all data and adding the checkboxes and plot buttons
"""
#first check if the table has been changed before clearing it
if self.mod_flag:
ret, saved = self._save_check()
if ret == QtGui.QMessageBox.Cancel:
return
self.current_table = None
settings = QtCore.QSettings()
settings.beginGroup(self.__column_settings)
for column in range(self.tableMain.columnCount()):
for row in range(self.tableMain.rowCount()):
if (column in self.run_cols):
item = QtGui.QTableWidgetItem()
item.setText('')
item.setToolTip('Runs can be colon delimited to coadd them')
self.tableMain.setItem(row, column, item)
elif (column in self.angle_cols):
item = QtGui.QTableWidgetItem()
item.setText('')
item.setToolTip('Angles are in degrees')
self.tableMain.setItem(row, column, item)
elif column == self.stitch_col:
check = QtGui.QCheckBox()
check.setCheckState(False)
check.setToolTip('If checked, the runs in this row will be stitched together')
item = QtGui.QWidget()
layout = QtGui.QHBoxLayout(item)
layout.addWidget(check)
layout.setAlignment(QtCore.Qt.AlignCenter)
layout.setSpacing(0)
layout.setContentsMargins(0, 0, 0, 0)
item.setLayout(layout)
item.setContentsMargins(0, 0, 0, 0)
self.tableMain.setCellWidget(row, self.stitch_col, item)
elif column == self.plot_col:
button = QtGui.QPushButton('Plot')
button.setProperty("row", row)
self.__reset_plot_button(button)
button.setToolTip('Plot the workspaces produced by processing this row.')
button.clicked.connect(self._plot_row)
item = QtGui.QWidget()
layout = QtGui.QHBoxLayout(item)
layout.addWidget(button)
layout.setAlignment(QtCore.Qt.AlignCenter)
layout.setSpacing(0)
layout.setContentsMargins(0, 0, 0, 0)
item.setLayout(layout)
item.setContentsMargins(0, 0, 0, 0)
self.tableMain.setCellWidget(row, self.plot_col, item)
else:
item = QtGui.QTableWidgetItem()
item.setText('')
self.tableMain.setItem(row, column, item)
vis_state = settings.value(str(column), True, type=bool)
self.shown_cols[column] = vis_state
if vis_state:
self.tableMain.showColumn(column)
else:
self.tableMain.hideColumn(column)
settings.endGroup()
del settings
self.tableMain.resizeColumnsToContents()
self.mod_flag = False
def _connect_slots(self):
"""
Connect the signals to the corresponding methods
"""
self.checkTickAll.stateChanged.connect(self._set_all_stitch)
self.comboInstrument.activated[int].connect(self._instrument_selected)
self.comboPolarCorrect.activated.connect(self._polar_corr_selected)
self.textRB.returnPressed.connect(self._populate_runs_list)
self.buttonAuto.clicked.connect(self._autofill)
self.buttonSearch.clicked.connect(self._populate_runs_list)
self.buttonClear.clicked.connect(self._initialise_table)
self.buttonProcess.clicked.connect(self._process)
self.buttonTransfer.clicked.connect(self._transfer)
self.buttonColumns.clicked.connect(self._choose_columns)
self.actionOpen_Table.triggered.connect(self._load_table)
self.actionReload_from_Disk.triggered.connect(self._reload_table)
self.actionSave.triggered.connect(self._save)
self.actionSave_As.triggered.connect(self._save_as)
self.actionSave_Workspaces.triggered.connect(self._save_workspaces)
self.actionClose_Refl_Gui.triggered.connect(self.close)
self.actionMantid_Help.triggered.connect(self._show_help)
self.actionAutofill.triggered.connect(self._autofill)
self.actionSearch_RB.triggered.connect(self._populate_runs_list)
self.actionClear_Table.triggered.connect(self._initialise_table)
self.actionProcess.triggered.connect(self._process)
self.actionTransfer.triggered.connect(self._transfer)
self.tableMain.cellChanged.connect(self._table_modified)
self.actionClear.triggered.connect(self._clear_cells)
self.actionPaste.triggered.connect(self._paste_cells)
self.actionCut.triggered.connect(self._cut_cells)
self.actionCopy.triggered.connect(self._copy_cells)
self.actionChoose_Columns.triggered.connect(self._choose_columns)
self.actionRefl_Gui_Options.triggered.connect(self._options_dialog)
def __valid_rb(self):
# Ensure that you cannot put zero in for an rb search
rbSearchValidator = QtGui.QIntValidator(self)
current_text = self.textRB.text()
rbSearchValidator.setBottom(1)
state = rbSearchValidator.validate(current_text, 0)[0]
if state == QtGui.QValidator.Acceptable:
return True
else:
self.textRB.clear()
if current_text:
logger.warning("RB search restricted to numbers > 0")
return False
def _populate_runs_list(self):
"""
Populate the list at the right with names of runs and workspaces from the archives
"""
# Clear existing
self.listMain.clear()
if self.__valid_rb():
"""
Use ICAT for a journal search based on the RB number
"""
active_session_id = None
if CatalogManager.numberActiveSessions() == 0:
# Execute the CatalogLoginDialog
login_alg = CatalogLoginDialog()
session_object = login_alg.getProperty("KeepAlive").value
active_session_id = session_object.getPropertyValue("Session")
# Fetch out an existing session id
active_session_id = CatalogManager.getActiveSessions()[-1].getSessionId() # TODO. This might be another catalog session, but at present there is no way to tell.
search_alg = AlgorithmManager.create('CatalogGetDataFiles')
search_alg.initialize()
search_alg.setChild(True) # Keeps the results table out of the ADS
search_alg.setProperty('InvestigationId', str(self.textRB.text()))
search_alg.setProperty('Session', active_session_id)
search_alg.setPropertyValue('OutputWorkspace', '_dummy')
search_alg.execute()
search_results = search_alg.getProperty('OutputWorkspace').value
self.__icat_file_map = {}
self.statusMain.clearMessage()
for row in search_results:
file_name = row['Name']
file_id = row['Id']
description = row['Description']
run_number = re.search('[1-9]\d+', file_name).group()
if bool(re.search('(raw)$', file_name, re.IGNORECASE)): # Filter to only display and map raw files.
title = (run_number + ': ' + description).strip()
self.__icat_file_map[title] = (file_id, run_number, file_name)
self.listMain.addItem(title)
self.listMain.sortItems()
del search_results
def _autofill(self):
"""
copy the contents of the selected cells to the row below as long as the row below contains a run number in the first cell
"""
col = 0
# make sure all selected cells are in the same row
sum = 0
howMany = len(self.tableMain.selectedItems())
for cell in self.tableMain.selectedItems():
sum = sum + self.tableMain.row(cell)
if (howMany):
selectedrow = self.tableMain.row(self.tableMain.selectedItems()[0])
if (sum / howMany == selectedrow):
startrow = selectedrow + 1
filled = 0
for cell in self.tableMain.selectedItems():
row = startrow
txt = cell.text()
while (self.tableMain.item(row, 0).text() != ''):
item = QtGui.QTableWidgetItem()
item.setText(txt)
self.tableMain.setItem(row, self.tableMain.column(cell), item)
row = row + 1
filled = filled + 1
if not filled:
QtGui.QMessageBox.critical(self.tableMain, 'Cannot perform Autofill',"No target cells to autofill. Rows to be filled should contain a run number in their first cell, and start from directly below the selected line.")
else:
QtGui.QMessageBox.critical(self.tableMain, 'Cannot perform Autofill',"Selected cells must all be in the same row.")
else:
QtGui.QMessageBox.critical(self.tableMain, 'Cannot perform Autofill',"There are no source cells selected.")
def _create_workspace_display_name(self, candidate):
"""
Create a display name from a workspace.
"""
if isinstance(mtd[candidate], WorkspaceGroup):
todisplay = candidate # No single run number for a group of workspaces.
else:
todisplay = groupGet(mtd[candidate], "samp", "run_number")
return todisplay
def _clear_cells(self):
"""
Clear the selected area of data
"""
cells = self.tableMain.selectedItems()
for cell in cells:
column = cell.column()
if column < self.stitch_col:
cell.setText('')
def _cut_cells(self):
"""
copy the selected cells then clear the area
"""
self._copy_cells()
self._clear_cells()
def _copy_cells(self):
"""
Copy the selected ranage of cells to the clipboard
"""
cells = self.tableMain.selectedItems()
if not cells:
print 'nothing to copy'
return
#first discover the size of the selection and initialise a list
mincol = cells[0].column()
if mincol > self.scale_col:
logger.error("Cannot copy, all cells out of range")
return
maxrow = -1
maxcol = -1
minrow = cells[0].row()
for cell in reversed(range(len(cells))):
col = cells[cell].column()
if col < self.stitch_col:
maxcol = col
maxrow = cells[cell].row()
break
colsize = maxcol - mincol + 1
rowsize = maxrow - minrow + 1
selection = [['' for x in range(colsize)] for y in range(rowsize)]
#now fill that list
for cell in cells:
row = cell.row()
col = cell.column()
if col < self.stitch_col:
selection[row - minrow][col - mincol] = str(cell.text())
tocopy = ''
for y in range(rowsize):
for x in range(colsize):
if x > 0:
tocopy += '\t'
tocopy += selection[y][x]
if y < (rowsize - 1):
tocopy += '\n'
self.clip.setText(str(tocopy))
def _paste_cells(self):
"""
Paste the contents of the clipboard to the table at the selected position
"""
pastedtext = self.clip.text()
if not pastedtext:
logger.warning("Nothing to Paste")
return
selected = self.tableMain.selectedItems()
if not selected:
logger.warning("Cannot paste, no editable cells selected")
return
pasted = pastedtext.splitlines()
pastedcells = []
for row in pasted:
pastedcells.append(row.split('\t'))
pastedcols = len(pastedcells[0])
pastedrows = len(pastedcells)
if len(selected) > 1:
#discover the size of the selection
mincol = selected[0].column()
if mincol > self.scale_col:
logger.error("Cannot copy, all cells out of range")
return
minrow = selected[0].row()
#now fill that list
for cell in selected:
row = cell.row()
col = cell.column()
if col < self.stitch_col and (col - mincol) < pastedcols and (row - minrow) < pastedrows and len(pastedcells[row - minrow]):
cell.setText(pastedcells[row - minrow][col - mincol])
elif selected:
#when only a single cell is selected, paste all the copied item up until the table limits
cell = selected[0]
currow = cell.row()
homecol = cell.column()
tablerows = self.tableMain.rowCount()
for row in pastedcells:
if len(row):
curcol = homecol
if currow < tablerows:
for col in row:
if curcol < self.stitch_col:
curcell = self.tableMain.item(currow, curcol)
curcell.setText(col)
curcol += 1
else:
#the row has hit the end of the editable cells
break
currow += 1
else:
#it's dropped off the bottom of the table
break
else:
logger.warning("Cannot paste, no editable cells selected")
def _transfer(self):
"""
Transfer run numbers to the table
"""
tup = ()
for idx in self.listMain.selectedItems():
split_title = re.split("th=|:", idx.text())
if len(split_title) != 3:
split_title = re.split(":", idx.text())
if len(split_title) != 2:
logger.warning('cannot transfer ' + idx.text() + ' title is not in the right form ')
else:
theta = 0
split_title.append(theta) # Append a dummy theta value.
tup = tup + (split_title,)
else:
tup = tup + (split_title,) # Tuple of lists containing (run number, title, theta)
tupsort=sorted(tup,key=itemgetter(1,2)) # now sorted by title then theta
row = 0
for key, group in itertools.groupby(tupsort, lambda x: x[1]): # now group by title
col = 0
run_angle_pairs_of_title = list() # for storing run_angle pairs all with the same title
for object in group: # loop over all with equal title
run_no = object[0]
angle = object[-1]
run_angle_pairs_of_title.append((run_no, angle))
for angle_key, group in itertools.groupby(run_angle_pairs_of_title, lambda x: x[1]):
runnumbers = "+".join(["%s" % pair[0] for pair in group])
# set the runnumber
item = QtGui.QTableWidgetItem()
item.setText(str(runnumbers))
self.tableMain.setItem(row, col, item)
# Set the angle
item = QtGui.QTableWidgetItem()
item.setText(str(angle_key))
self.tableMain.setItem(row, col + 1, item)
# Set the transmission
item = QtGui.QTableWidgetItem()
item.setText(self.textRuns.text())
self.tableMain.setItem(row, col + 2, item)
col = col + 5
if col >= 11:
col = 0
row = row + 1
if self.__icat_download:
"""
If ICAT is being used for download, then files must be downloaded at the same time as they are transfered.
"""
contents = str(idx.text()).strip()
file_id, runnumber, file_name = self.__icat_file_map[contents]
active_session_id = CatalogManager.getActiveSessions()[-1].getSessionId() # TODO. This might be another catalog session, but at present there is no way to tell.
save_location = config['defaultsave.directory']
CatalogDownloadDataFiles(file_id, FileNames=file_name, DownloadPath=save_location, Session=active_session_id)
current_search_dirs= config.getDataSearchDirs()
if not save_location in current_search_dirs:
config.appendDataSearchDir(save_location)
def _set_all_stitch(self,state):
"""
Set the checkboxes in the Stitch? column to the same
"""
for row in range(self.tableMain.rowCount()):
self.tableMain.cellWidget(row, self.stitch_col).children()[1].setCheckState(state)
def __checked_row_stiched(self, row):
return self.tableMain.cellWidget(row, self.stitch_col).children()[1].checkState() > 0
def _process(self):
"""
Process has been pressed, check what has been selected then pass the selection (or whole table) to quick
"""
#--------- If "Process" button pressed, convert raw files to IvsLam and IvsQ and combine if checkbox ticked -------------
try:
willProcess = True
rows = self.tableMain.selectionModel().selectedRows()
rowIndexes=[]
for idx in rows:
rowIndexes.append(idx.row())
if not len(rowIndexes):
reply = QtGui.QMessageBox.question(self.tableMain, 'Process all rows?',"This will process all rows in the table. Continue?", QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.No:
logger.notice("Cancelled!")
willProcess = False
else:
rowIndexes = range(self.tableMain.rowCount())
if willProcess:
for row in rowIndexes: # range(self.tableMain.rowCount()):
runno = []
loadedRuns = []
wksp = []
overlapLow = []
overlapHigh = []
theta = [0, 0, 0]
if (self.tableMain.item(row, 0).text() != ''):
self.statusMain.showMessage("Processing row: " + str(row + 1))
logger.debug("Processing row: " + str(row + 1))
for i in range(3):
run_entry = str(self.tableMain.item(row, i * 5).text())
if (run_entry != ''):
runno.append(run_entry)
ovLow = str(self.tableMain.item(row, (i * 5) + 3).text())
if (ovLow != ''):
overlapLow.append(float(ovLow))
ovHigh = str(self.tableMain.item(row, (i * 5) + 4).text())
if (ovHigh != ''):
overlapHigh.append(float(ovHigh))
# Determine resolution
if (self.tableMain.item(row, 15).text() == ''):
loadedRun = None
if load_live_runs.is_live_run(runno[0]):
loadedRun = load_live_runs.get_live_data(config['default.instrument'], frequency = self.live_freq, accumulation = self.live_method)
else:
Load(Filename=runno[0], OutputWorkspace="run")
loadedRun = mtd["run"]
two_theta_str = str(self.tableMain.item(row, 1).text())
try:
two_theta = None
if len(two_theta_str) > 0:
two_theta = float(two_theta_str)
dqq, two_theta = CalculateResolution(Workspace = loadedRun, TwoTheta = two_theta)
#Put the calculated resolution into the table
resItem = QtGui.QTableWidgetItem()
resItem.setText(str(dqq))
self.tableMain.setItem(row, 15, resItem)
#Update the value for two_theta in the table
ttItem = QtGui.QTableWidgetItem()
ttItem.setText(str(two_theta))
self.tableMain.setItem(row, 1, ttItem)
logger.notice("Calculated resolution: " + str(dqq))
except IndexError:
self.statusMain.clearMessage()
logger.error("Cannot calculate resolution owing to unknown log properties. dq/q will need to be manually entered.")
return
else:
dqq = float(self.tableMain.item(row, 15).text())
# Populate runlist
first_wq = None
for i in range(len(runno)):
theta, qmin, qmax, wlam, wq = self._do_run(runno[i], row, i)
if not first_wq:
first_wq = wq # Cache the first Q workspace
theta = round(theta, 3)
qmin = round(qmin, 3)
qmax = round(qmax, 3)
wksp.append(wq.name())
if (self.tableMain.item(row, i * 5 + 1).text() == ''):
item = QtGui.QTableWidgetItem()
item.setText(str(theta))
self.tableMain.setItem(row, i * 5 + 1, item)
if (self.tableMain.item(row, i * 5 + 3).text() == ''):
item = QtGui.QTableWidgetItem()
item.setText(str(qmin))
self.tableMain.setItem(row, i * 5 + 3, item)
overlapLow.append(qmin)
if (self.tableMain.item(row, i * 5 + 4).text() == ''):
item = QtGui.QTableWidgetItem()
if i == len(runno) - 1:
# allow full high q-range for last angle
qmax = 4 * math.pi / ((4 * math.pi / qmax * math.sin(theta * math.pi / 180)) - 0.5) * math.sin(theta * math.pi / 180)
item.setText(str(qmax))
self.tableMain.setItem(row, i * 5 + 4, item)
overlapHigh.append(qmax)
if wksp[i].find(',') > 0 or wksp[i].find(':') > 0:
wksp[i] = first_wq.name()
#Scale each run
if self.tableMain.item(row, self.scale_col).text():
Scale(InputWorkspace=wksp[i], OutputWorkspace=wksp[i], Factor=1 / float(self.tableMain.item(row, self.scale_col).text()))
if self.__checked_row_stiched(row):
if (len(runno) == 1):
logger.notice("Nothing to combine for processing row : " + str(row))
else:
w1 = getWorkspace(wksp[0])
w2 = getWorkspace(wksp[-1])
if (len(runno) == 2):
outputwksp = runno[0] + '_' + runno[1][3:5]
else:
outputwksp = runno[0] + '_' + runno[-1][3:5]
begoverlap = w2.readX(0)[0]
# get Qmax
if (self.tableMain.item(row, i * 5 + 4).text() == ''):
overlapHigh = 0.3 * max(w1.readX(0))
Qmin = min(w1.readX(0))
Qmax = max(w2.readX(0))
wcomb = combineDataMulti(wksp, outputwksp, overlapLow, overlapHigh, Qmin, Qmax, -dqq, 1, keep=True)
# Enable the plot button
plotbutton = self.tableMain.cellWidget(row, self.plot_col).children()[1]
plotbutton.setProperty('runno',runno)
plotbutton.setProperty('overlapLow', overlapLow)
plotbutton.setProperty('overlapHigh', overlapHigh)
plotbutton.setProperty('wksp', wksp)
plotbutton.setEnabled(True)
self.statusMain.clearMessage()
self.accMethod = None
self.statusMain.clearMessage()
except:
self.statusMain.clearMessage()
raise
def _plot(self, plotbutton):
"""
Plot the row belonging to the selected button
"""
if not isinstance(plotbutton, QtGui.QPushButton):
logger.error("Problem accessing cached data: Wrong data type passed, expected QtGui.QPushbutton")
return
import unicodedata
#make sure the required data can be retrieved properly
try:
runno_u = plotbutton.property('runno')
runno = []
for uni in runno_u:
runno.append(unicodedata.normalize('NFKD', uni).encode('ascii','ignore'))
wksp_u = plotbutton.property('wksp')
wksp = []
for uni in wksp_u:
wksp.append(unicodedata.normalize('NFKD', uni).encode('ascii','ignore'))
overlapLow = plotbutton.property('overlapLow')
overlapHigh = plotbutton.property('overlapHigh')
row = plotbutton.property('row')
g = ['g1', 'g2', 'g3']
wkspBinned = []
w1 = getWorkspace(wksp[0])
w2 = getWorkspace(wksp[len(wksp) - 1])
dqq = float(self.tableMain.item(row, 15).text())
except:
logger.error("Unable to plot row, required data couldn't be retrieved")
self.__reset_plot_button(plotbutton)
return
for i in range(len(runno)):
ws_name_binned = wksp[i] + '_binned'
ws = getWorkspace(wksp[i])
if len(overlapLow):
Qmin = overlapLow[0]
else:
Qmin = min(w1.readX(0))
if len(overlapHigh):
Qmax = overlapHigh[len(overlapHigh) - 1]
else:
Qmax = max(w2.readX(0))
Rebin(InputWorkspace=str(wksp[i]), Params=str(overlapLow[i]) + ',' + str(-dqq) + ',' + str(overlapHigh[i]), OutputWorkspace=ws_name_binned)
wkspBinned.append(ws_name_binned)
wsb = getWorkspace(ws_name_binned)
Imin = min(wsb.readY(0))
Imax = max(wsb.readY(0))
if canMantidPlot:
g[i] = plotSpectrum(ws_name_binned, 0, True)
titl = groupGet(ws_name_binned, 'samp', 'run_title')
if (i > 0):
mergePlots(g[0], g[i])
if (type(titl) == str):
g[0].activeLayer().setTitle(titl)
g[0].activeLayer().setAxisScale(Layer.Left, Imin * 0.1, Imax * 10, Layer.Log10)
g[0].activeLayer().setAxisScale(Layer.Bottom, Qmin * 0.9, Qmax * 1.1, Layer.Log10)
g[0].activeLayer().setAutoScale()
# Create and plot stitched outputs
if self.__checked_row_stiched(row):
if (len(runno) == 2):
outputwksp = runno[0] + '_' + runno[1][3:5]
else:
outputwksp = runno[0] + '_' + runno[2][3:5]
if not getWorkspace(outputwksp, report_error=False):
# Stitching has not been done as part of processing, so we need to do it here.
wcomb = combineDataMulti(wkspBinned, outputwksp, overlapLow, overlapHigh, Qmin, Qmax, -dqq, 1, keep=True)
Qmin = min(getWorkspace(outputwksp).readX(0))
Qmax = max(getWorkspace(outputwksp).readX(0))
if canMantidPlot:
gcomb = plotSpectrum(outputwksp, 0, True)
titl = groupGet(outputwksp, 'samp', 'run_title')
gcomb.activeLayer().setTitle(titl)
gcomb.activeLayer().setAxisScale(Layer.Left, 1e-8, 100.0, Layer.Log10)
gcomb.activeLayer().setAxisScale(Layer.Bottom, Qmin * 0.9, Qmax * 1.1, Layer.Log10)
def __name_trans(self, transrun):
"""
From a comma or colon separated string of run numbers
construct an output workspace name for the transmission workspace that fits the form
TRANS_{trans_1}_{trans_2}
"""
if bool(re.search("^(TRANS)", transrun)):
# The user has deliberately tried to supply the transmission run directly
return transrun
else:
split_trans = re.split(',|:', transrun)
if len(split_trans) == 0:
return None
name = 'TRANS'
for t in split_trans:
name += '_' + str(t)
return name
def _do_run(self, runno, row, which):
"""
Run quick on the given run and row
"""
g = ['g1', 'g2', 'g3']
transrun = str(self.tableMain.item(row, (which * 5) + 2).text())
# Formulate a WS Name for the processed transmission run.
transrun_named = self.__name_trans(transrun)
# Look for existing transmission workspaces that match the name
transmission_ws = None
if mtd.doesExist(transrun_named) and mtd[transrun_named].getAxis(0).getUnit().unitID() == "Wavelength":
logger.notice('Reusing transmission workspace ' + transrun_named)
transmission_ws = mtd[transrun_named]
angle = str(self.tableMain.item(row, which * 5 + 1).text())
# Explicitly set the angle to None so that the workflow algorithm doesn't try to interpret it.
if not angle:
angle = None
loadedRun = runno
if load_live_runs.is_live_run(runno):
load_live_runs.get_live_data(config['default.instrument'], frequency = self.live_freq, accumulation = self.live_method)
wlam, wq, th = None, None, None
# Only make a transmission workspace if we need one.
if transrun and not transmission_ws:
converter = ConvertToWavelength(transrun)
trans_run_names = converter.get_name_list()
size = converter.get_ws_list_size()
out_ws_name = transrun_named
if size == 1:
trans1 = converter.get_workspace_from_list(0)
transmission_ws = CreateTransmissionWorkspaceAuto(FirstTransmissionRun=trans1, OutputWorkspace=out_ws_name,Params=0.02, StartOverlap=10.0, EndOverlap=12.0 )
elif size == 2:
trans1 = converter.get_workspace_from_list(0)
trans2 = converter.get_workspace_from_list(1)
transmission_ws = CreateTransmissionWorkspaceAuto(FirstTransmissionRun=trans1, OutputWorkspace=out_ws_name, SecondTransmissionRun=trans2,Params=0.02, StartOverlap=10.0, EndOverlap=12.0 )
else:
raise RuntimeError("Up to 2 transmission runs can be specified. No more than that.")
if self.alg_use:
#Load the runs required ConvertToWavelength will deal with the transmission runs, while .to_workspace will deal with the run itself
ws = ConvertToWavelength.to_workspace(loadedRun, ws_prefix="")
wq, wlam, th = ReflectometryReductionOneAuto(InputWorkspace=ws, FirstTransmissionRun=transmission_ws, thetaIn=angle, OutputWorkspace=runno+'_IvsQ', OutputWorkspaceWavelength=runno+'_IvsLam',)
cleanup()
else:
wlam, wq, th = quick(loadedRun, trans=transmission_ws, theta=angle, tof_prefix="")
try:
tof_group = mtd["TOF"]
if not tof_group.contains(loadedRun):
tof_group.add(loadedRun)
except KeyError:
tof_group = GroupWorkspaces(InputWorkspaces=loadedRun, OutputWorkspace="TOF")
if ':' in runno:
runno = runno.split(':')[0]
if ',' in runno:
runno = runno.split(',')[0]
inst = groupGet(wq, 'inst')
lmin = inst.getNumberParameter('LambdaMin')[0] + 1
lmax = inst.getNumberParameter('LambdaMax')[0] - 2
qmin = 4 * math.pi / lmax * math.sin(th * math.pi / 180)
qmax = 4 * math.pi / lmin * math.sin(th * math.pi / 180)
return th, qmin, qmax, wlam, wq
def _save_table_contents(self, filename):
"""
Save the contents of the table
"""
try:
writer = csv.writer(open(filename, "wb"))
for row in range(self.tableMain.rowCount()):
rowtext = []
for column in range(self.tableMain.columnCount() - 2):
rowtext.append(self.tableMain.item(row, column).text())
if (len(rowtext) > 0):
writer.writerow(rowtext)
self.current_table = filename
logger.notice("Saved file to " + filename)
self.mod_flag = False
except:
return False
self.mod_flag = False
return True
def _save(self, failsave = False):
"""
Save the table, showing no interface if not necessary. This also provides the failing save functionality.
"""
filename = ''
if failsave:
#this is an emergency autosave as the program is failing
logger.error("The ISIS Reflectonomy GUI has encountered an error, it will now attempt to save a copy of your work.")
msgBox = QtGui.QMessageBox()
msgBox.setText("The ISIS Reflectonomy GUI has encountered an error, it will now attempt to save a copy of your work.\nPlease check the log for details.")
msgBox.setStandardButtons(QtGui.QMessageBox.Ok)
msgBox.setIcon(QtGui.QMessageBox.Critical)
msgBox.setDefaultButton(QtGui.QMessageBox.Ok)
msgBox.setEscapeButton(QtGui.QMessageBox.Ok)
msgBox.exec_()
import datetime
failtime = datetime.datetime.today().strftime('%Y-%m-%d_%H-%M-%S')
if self.current_table:
filename = self.current_table.rsplit('.',1)[0] + "_recovered_" + failtime + ".tbl"
else:
mantidDefault = config['defaultsave.directory']
if os.path.exists(mantidDefault):
filename = os.path.join(mantidDefault,"mantid_reflectometry_recovered_" + failtime + ".tbl")
else:
import tempfile
tempDir = tempfile.gettempdir()
filename = os.path.join(tempDir,"mantid_reflectometry_recovered_" + failtime + ".tbl")
else:
#this is a save-on-quit or file->save
if self.current_table: