def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
saveFavoriteFile(str(fn), favfilepath)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
saveFavoriteFile(str(fn), favfilepath)
return
def start_download(self, request):
if not self.gui:
return
url = unicode(request.url().toString())
cf = self.get_cookies()
filename = get_download_filename(url, cf)
ext = os.path.splitext(filename)[1][1:].lower()
filename = ascii_filename(filename[:60] + '.' + ext)
if ext not in BOOK_EXTENSIONS:
if ext == 'acsm':
from calibre.gui2.dialogs.confirm_delete import confirm
if not confirm(
'<p>' +
_('This ebook is a DRMed EPUB file. '
'You will be prompted to save this file to your '
'computer. Once it is saved, open it with '
'<a href="http://www.adobe.com/products/digitaleditions/">'
'Adobe Digital Editions</a> (ADE).<p>ADE, in turn '
'will download the actual ebook, which will be a '
'.epub file. You can add this book to calibre '
'using "Add Books" and selecting the file from '
'the ADE library folder.'), 'acsm_download', self):
return
home = os.path.expanduser('~')
name = QFileDialog.getSaveFileName(
self, _('File is not a supported ebook type. Save to disk?'),
os.path.join(home, filename), '*.*')
if name:
name = unicode(name)
self.gui.download_ebook(url, cf, name, name, False)
else:
self.gui.download_ebook(url, cf, filename, tags=self.tags)
def saveFavorite(self):
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def saveFavorite(self):
"""
Save favorite file in a user chosen location
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def rezip_epub2(self, epub, titre_dialogue="Enregistrer l'epub détatoué sous :"):
self.setLabelText('Reconstruction de l\'epub')
QtGui.QApplication.processEvents()
# choix du nom de l'epub
epub2 = QFileDialog.getSaveFileName(None, titre_dialogue, epub, 'epub(*.epub)')
if zipfile.is_zipfile(epub):
try:
zepub = zipfile.ZipFile(epub2, mode="w",
compression=zipfile.ZIP_DEFLATED, allowZip64=True)
# d'abord le mimetype non compressé.
zepub.write(os.path.join(self.dirtemp.name, "mimetype"), arcname="mimetype",
compress_type=zipfile.ZIP_STORED)
# puis les autres fichiers
exclude_files = ['.DS_Store', 'mimetype']
for root, _dirs, files in os.walk(self.dirtemp.name):
for fn in files:
if fn in exclude_files:
continue
absfn = os.path.join(root, fn)
zfn = os.path.relpath(absfn, self.dirtemp.name).replace(os.sep, '/')
zepub.write(absfn, zfn)
zepub.close()
except:
log('Impossible de rezipper cet epub.')
return
def start_download(self, request):
if not self.gui:
return
url = unicode(request.url().toString())
cf = self.get_cookies()
filename = get_download_filename(url, cf)
ext = os.path.splitext(filename)[1][1:].lower()
filename = ascii_filename(filename[:60] + '.' + ext)
if ext not in BOOK_EXTENSIONS:
if ext == 'acsm':
from calibre.gui2.dialogs.confirm_delete import confirm
if not confirm('<p>' + _('This ebook is a DRMed EPUB file. '
'You will be prompted to save this file to your '
'computer. Once it is saved, open it with '
'<a href="http://www.adobe.com/products/digitaleditions/">'
'Adobe Digital Editions</a> (ADE).<p>ADE, in turn '
'will download the actual ebook, which will be a '
'.epub file. You can add this book to calibre '
'using "Add Books" and selecting the file from '
'the ADE library folder.'),
'acsm_download', self):
return
home = os.path.expanduser('~')
name = QFileDialog.getSaveFileName(self,
_('File is not a supported ebook type. Save to disk?'),
os.path.join(home, filename),
'*.*')
if name:
name = unicode(name)
self.gui.download_ebook(url, cf, name, name, False)
else:
self.gui.download_ebook(url, cf, filename, tags=self.tags)
def btnCardLocation_Clicked(self):
try:
savePath = str(QFileDialog.getSaveFileName(self, "Save as"))
tempPath = savePath
if len(savePath
) > 8: #teensy requires names of less than 8 characters
savePath = os.path.join(os.path.dirname(savePath),
os.path.basename(savePath)[:8])
__SONGS_temp_ = {
os.path.basename(tempPath): os.path.basename(savePath)
}
settings[0] = savePath
if not os.path.exists(settings[0]):
os.makedirs(settings[0])
shelfFile = shelve.open('GUIconfig')
if (not '__SONGS__' in shelfFile.keys()):
shelfFile['__SONGS__'] = {}
__SONGS_temp_2 = shelfFile['__SONGS__']
if not list(__SONGS_temp_.keys())[0] in list(
__SONGS_temp_2.keys()):
__SONGS_temp_2.update(__SONGS_temp_)
shelfFile['__SONGS__'] = __SONGS_temp_2
self.ui.SelectSong.addItems(list(__SONGS_temp_.keys()))
else:
pass
# print("key exists not adding")
shelfFile.close()
self.ui.lineEdit.setText(os.path.basename(tempPath))
except Exception as e:
pass
def export_bookmarks(self):
filename = QFileDialog.getSaveFileName(self, _("Export Bookmarks"),
'%s%suntitled.pickle' % (os.getcwdu(), os.sep),
_("Saved Bookmarks (*.pickle)"))
if filename == '':
return
with open(filename, 'w') as fileobj:
cPickle.dump(self._model.bookmarks, fileobj)
def export_bookmarks(self):
filename = QFileDialog.getSaveFileName(self, _("Export Bookmarks"),
'%s%suntitled.pickle' % (os.getcwdu(), os.sep),
_("Saved Bookmarks (*.pickle)"))
if not filename:
return
with open(filename, 'w') as fileobj:
cPickle.dump(self.get_bookmarks(), fileobj)
def Save(self):
d = QFileDialog(self)
s = d.getSaveFileName()
l = len(self.mt.Images)
for i in xrange(l):
self.mt.Images[i].save(s+'.'+str(i)+'.png')
f = open(s,"w")
f.write(str(l))
f.close()
def saveParserAs(self):
filename = str(
QFileDialog.getSaveFileName(self,
caption="%s - Save a parser" %
QApplication.applicationName(),
directory=str("."),
filter=str("XML files (*.xml)")))
if not filename:
return
misc.saveAsXML(self.parser, filename)
self.filename = filename
self.updateStatus("Saved parser to file %s" % filename)
def saveToFile(self):
fdiag = QFileDialog()
selectedFilter = QString()
if foundPandas:
filt = self.tr("Excel Open XML Document (*.xlsx);;Portable Network Graphics (*.png)")
else:
filt = self.tr("Portable Network Graphics (*.png)")
fileName = fdiag.getSaveFileName(self, self.tr("Save Data As"),
datetime.now().strftime('%Y-%m-%d-T%H%M%S-') + self.modeAscii,
filt, selectedFilter)
if len(fileName) == 0:
return
if 'png' in selectedFilter:
if fileName[-4:] == '.png':
fileName = fileName[0:-4]
px = QPixmap.grabWidget(self.graphGrp)
px.save(fileName + '.png', "PNG")
return
if fileName[-5:] == '.xlsx':
fileName = fileName[0:-5]
data = self.excelData.getData()
if len(data) == 0:
mb = QMessageBox()
mb.setIcon(QMessageBox.Warning)
mb.setWindowTitle(self.tr('Warning'))
mb.setText(self.tr('No data exists. No output file has been produced.'))
mb.exec_()
return
if data.ndim == 1: #Bad workaround if only one line exists
add = []
for idx in range(0,len(data)):
add.append(0)
data = np.vstack((data, np.array(add)))
df = pandas.DataFrame(data, columns=['Frequency', self.modeTuple[0], self.modeTuple[1]])
df.to_excel(str(fileName) + '.xlsx', index=False)
def saveStrandSequence(self):
"""
Save the strand sequence entered in the Strand text edit in the
specified file.
"""
if not self.sequenceFileName:
sdir = env.prefs[workingDirectory_prefs_key]
else:
sdir = self.sequenceFileName
fileName = QFileDialog.getSaveFileName(
self,
"Save Strand Sequence As ...",
sdir,
"Strand Sequence File (*.txt)"
)
if fileName:
fileName = str(fileName)
if fileName[-4] != '.':
fileName += '.txt'
if os.path.exists(fileName):
# ...and if the "Save As" file exists...
# ... confirm overwrite of the existing file.
ret = QMessageBox.warning(
self,
"Save Strand Sequence...",
"The file \"" + fileName + "\" already exists.\n"\
"Do you want to overwrite the existing file or cancel?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1 ) # Escape == button 1
if ret == 1:
# The user cancelled
return
# write the current set of element colors into a file
self._writeStrandSequenceFile(
fileName,
str(self.sequenceTextEdit.toPlainText()))
return
def MakeGcode(self):
path = QFileDialog.getSaveFileName(self, u"选择保存路径", "", " (*.nc)")
if path == "":
QMessageBox.warning(self, u"发生错误", u"路径错误！！")
return
f = open(path, 'w')
f.write("M5\n")
for i in range(self.resultImage.width()):
flag = False
#检测这一行是否有点
for j in range(self.resultImage.height()):
if self.resultImage.pixelIndex(i, j) < 128:
flag = True
break
#如果这一行都没有点则跳过这一行
if flag:
f.write("G0 Y%f\n" % (i * self.pixDoubleSpinBox.value()))
else:
continue
if (i % 2) > 0:
for j in range(self.resultImage.height()):
if self.resultImage.pixelIndex(i, j) < 128:
f.write("G0 X%f\n" %
(j * self.pixDoubleSpinBox.value()))
f.write("M3\n")
f.write("G4 P%f\n" % self.timeDoubleSpinBox.value())
f.write("M5\n")
else:
for j in range(self.resultImage.height())[::-1]:
if self.resultImage.pixelIndex(i, j) < 128:
f.write("G0 X%f\n" %
(j * self.pixDoubleSpinBox.value()))
f.write("M3\n")
f.write("G4 P%f\n" % self.timeDoubleSpinBox.value())
f.write("M5\n")
f.write("M5\n")
f.write("G0 X0 Y0\n")
f.close()
QMessageBox.information(self, u"成功", u"生成G代码文件成功！！")
def write_element_rgb_table(self):
"""
Save the current set of element preferences into an external file --
currently only r,g,b color of each element will be saved.
"""
if not self.fileName:
from utilities.prefs_constants import workingDirectory_prefs_key
sdir = env.prefs[workingDirectory_prefs_key]
else:
sdir = self.fileName
fn = QFileDialog.getSaveFileName(self, "Save Element Colors As ...",
sdir, "Element Color File (*.txt)")
if fn:
fn = str(fn)
if fn[-4] != '.':
fn += '.txt'
import os
if os.path.exists(fn): # ...and if the "Save As" file exists...
# ... confirm overwrite of the existing file.
ret = QMessageBox.warning(
self,
"Save Element Colors...",
"The file \"" + fn + "\" already exists.\n"
"Do you want to overwrite the existing file or cancel?",
"&Overwrite",
"&Cancel",
"",
0, # Enter == button 0
1) # Escape == button 1
if ret == 1: # The user cancelled
return
# write the current set of element colors into a file
saveElementColors(fn, self.elemTable.getAllElements())
env.history.message("Element colors saved in file: [" + fn + "]")
#After saving a file, reset the flag
self.isFileSaved = True
def write_element_rgb_table(self):
"""
Save the current set of element preferences into an external file --
currently only r,g,b color of each element will be saved.
"""
if not self.fileName:
from utilities.prefs_constants import workingDirectory_prefs_key
sdir = env.prefs[workingDirectory_prefs_key]
else:
sdir = self.fileName
fn = QFileDialog.getSaveFileName(
self,
"Save Element Colors As ...",
sdir,
"Element Color File (*.txt)"
)
if fn:
fn = str(fn)
if fn[-4] != '.':
fn += '.txt'
import os
if os.path.exists(fn): # ...and if the "Save As" file exists...
# ... confirm overwrite of the existing file.
ret = QMessageBox.warning( self, "Save Element Colors...",
"The file \"" + fn + "\" already exists.\n"
"Do you want to overwrite the existing file or cancel?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1 ) # Escape == button 1
if ret == 1: # The user cancelled
return
# write the current set of element colors into a file
saveElementColors(fn, self.elemTable.getAllElements())
env.history.message("Element colors saved in file: [" + fn + "]")
#After saving a file, reset the flag
self.isFileSaved = True
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
#Check to see if favfilepath exists first
if not os.path.exists(favfilepath):
msg = "%s does not exist" % favfilepath
env.history.message(cmd + msg)
return
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
saveLocation, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
#remember this directory
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def _saveImage(self):
filename = QFileDialog.getSaveFileName(self, "Save FITS file", self._save_dir,
"FITS files(*.fits *.FITS *fts *FTS)")
filename = str(filename)
if not filename:
return
busy = BusyIndicator()
self._imgman.showMessage("""Writing FITS image %s""" % filename, 3000)
QApplication.flush()
try:
self.image.save(filename)
except Exception as exc:
busy = None
traceback.print_exc()
self._imgman.showErrorMessage("""Error writing FITS image %s: %s""" % (filename, str(sys.exc_info()[1])))
return None
self.renderControl().startSavingConfig(filename)
self.setName(self.image.name)
self._qa_save.setVisible(False)
self._wsave.hide()
busy = None
def saveAnimation(self, listOfAnimatedElements, description=""):
"""
TODO: Doesn't work. Implement.
Serializes the animation after showing the user a dialog to
choose where to do so.
:param listOfAnimatedElements: The list of objects which compose this
animation.
:type listOfAnimatedElements: [Animation2]
.
:param fileName: The name of the file in which this animation
should be saved.
:type fileName: str
:param description: (optional) Brief description for this animation.
:type description: str
"""
filename = QFileDialog.getSaveFileName(parent=None,
caption="Save animation layer",
filter=("All Files (*.*)"))
# print filename
pass
def saveToFile(self):
fileName = QFileDialog.getSaveFileName(
self, "Open Points File", "",
"All Files (*);;Text Files (*.txt);;Excel (*.xlsx)", "")
if fileName[-4:] == ".txt":
f = open(fileName, 'w')
f.write(" Y X \n")
for i, j in self.provisionals.iteritems():
f.write(i + ": " + " " + str(round(float(j.y), 3)) +
" " + str(round(float(j.x), 3)) + "\n\n")
f.close()
elif fileName[-5:] == ".xlsx":
fileName = str(fileName)
workbook = xlsxwriter.Workbook(fileName)
worksheet = workbook.add_worksheet()
i = 0
for nm, j in sorted(self.provisionals.iteritems()):
worksheet.write(i, 0, nm)
worksheet.write(i, 1, (round(float(j.y), 3)))
worksheet.write(i, 2, (round(float(j.x), 3)))
i += 1
workbook.close()
def saveToFile(self):
fileName = QFileDialog.getSaveFileName(self,
"Open Points File",
"",
"All Files (*);;Text Files (*.txt);;Excel (*.xlsx)", "")
if fileName[-4:]==".txt":
f = open(fileName, 'w')
f.write(" Y X \n")
for i,j in self.provisionals.iteritems():
f.write(i +": "+" "+ str(round(float(j.y),3))+" "+ str(round(float(j.x),3))+"\n\n")
f.close()
elif fileName[-5:]==".xlsx":
fileName=str(fileName)
workbook = xlsxwriter.Workbook(fileName)
worksheet = workbook.add_worksheet()
i=0
for nm,j in sorted(self.provisionals.iteritems()):
worksheet.write(i,0, nm)
worksheet.write(i,1, (round(float(j.y),3)))
worksheet.write(i,2, (round(float(j.x),3)))
i+=1
workbook.close()
def saveAnimation(self, listOfAnimatedElements, description=""):
"""
TODO: Doesn't work. Implement.
Serializes the animation after showing the user a dialog to
choose where to do so.
:param listOfAnimatedElements: The list of objects which compose this
animation.
:type listOfAnimatedElements: [Animation2]
.
:param fileName: The name of the file in which this animation
should be saved.
:type fileName: str
:param description: (optional) Brief description for this animation.
:type description: str
"""
filename = QFileDialog.getSaveFileName(
parent = None,
caption = "Save animation layer",
filter=("All Files (*.*)"));
#print filename
pass
def _select_create_dialog(self):
path = str(QFileDialog.getSaveFileName(self, "Create new purrlog", self.create_path))
if path:
self._validate_create_filename(path)
def __init__(self, title=_('Choose Files'),
filters=[],
add_all_files_filter=True,
parent=None,
modal=True,
name='',
mode=QFileDialog.ExistingFiles,
default_dir=u'~',
no_save_dir=False,
combine_file_and_saved_dir=False
):
QObject.__init__(self)
ftext = ''
if filters:
for filter in filters:
text, extensions = filter
extensions = ['*'+(i if i.startswith('.') else '.'+i) for i in
extensions]
ftext += '%s (%s);;'%(text, ' '.join(extensions))
if add_all_files_filter or not ftext:
ftext += 'All files (*)'
if ftext.endswith(';;'):
ftext = ftext[:-2]
self.dialog_name = name if name else 'dialog_' + title
self.selected_files = None
self.fd = None
if combine_file_and_saved_dir:
bn = os.path.basename(default_dir)
prev = dynamic.get(self.dialog_name,
expanduser(u'~'))
if os.path.exists(prev):
if os.path.isfile(prev):
prev = os.path.dirname(prev)
else:
prev = expanduser(u'~')
initial_dir = os.path.join(prev, bn)
elif no_save_dir:
initial_dir = expanduser(default_dir)
else:
initial_dir = dynamic.get(self.dialog_name,
expanduser(default_dir))
if not isinstance(initial_dir, basestring):
initial_dir = expanduser(default_dir)
if not initial_dir or (not os.path.exists(initial_dir) and not (
mode == QFileDialog.AnyFile and (no_save_dir or combine_file_and_saved_dir))):
initial_dir = select_initial_dir(initial_dir)
self.selected_files = []
use_native_dialog = 'CALIBRE_NO_NATIVE_FILEDIALOGS' not in os.environ
with SanitizeLibraryPath():
opts = QFileDialog.Option()
if not use_native_dialog:
opts |= QFileDialog.DontUseNativeDialog
if mode == QFileDialog.AnyFile:
f = unicode(QFileDialog.getSaveFileName(parent, title,
initial_dir, ftext, "", opts))
if f:
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFile:
f = unicode(QFileDialog.getOpenFileName(parent, title,
initial_dir, ftext, "", opts))
if f and os.path.exists(f):
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFiles:
fs = QFileDialog.getOpenFileNames(parent, title, initial_dir,
ftext, "", opts)
for f in fs:
f = unicode(f)
if not f:
continue
if not os.path.exists(f):
# QFileDialog for some reason quotes spaces
# on linux if there is more than one space in a row
f = unquote(f)
if f and os.path.exists(f):
self.selected_files.append(f)
else:
if mode == QFileDialog.Directory:
opts |= QFileDialog.ShowDirsOnly
f = unicode(QFileDialog.getExistingDirectory(parent, title, initial_dir, opts))
if os.path.exists(f):
self.selected_files.append(f)
if self.selected_files:
self.selected_files = [unicode(q) for q in self.selected_files]
saved_loc = self.selected_files[0]
if os.path.isfile(saved_loc):
saved_loc = os.path.dirname(saved_loc)
if not no_save_dir:
dynamic[self.dialog_name] = saved_loc
self.accepted = bool(self.selected_files)
class MainWidget(QWidget):
def __init__(self):
QWidget.__init__(self)
# define periodic table widget for element selection
self.periodicTableWidget = widgets.PeriodicTableDialog()
# initial molecule Zmatrix (can be empty)
# self.inp = []
self.inp = [['H'],
['O', 1, 0.9],
['O', 2, 1.4, 1, 105.],
['H', 3, 0.9, 2, 105., 1, 120.]]
self.atomList = []
self.highList = []
self.labelList = []
self.fast = False
# define & initialize ZMatModel that will contain Zmatrix data
self.ZMatModel = QStandardItemModel(len(self.inp), 7, self)
self.ZMatTable = QTableView(self)
self.ZMatTable.setModel(self.ZMatModel)
self.ZMatTable.setFixedWidth(325)
#self.ZMatTable.installEventFilter(self)
#self.ZMatModel.installEventFilter(self)
self.ZMatModel.setHorizontalHeaderLabels(['atom','','bond','','angle','','dihedral'])
for j, width in enumerate([40, 22, 65, 22, 65, 22, 65]):
self.ZMatTable.setColumnWidth(j, width)
# populate the ZMatModel
self.populateZMatModel()
#define Menu bar menus and their actions
self.menuBar = QMenuBar(self)
fileMenu = self.menuBar.addMenu('&File')
editMenu = self.menuBar.addMenu('&Edit')
viewMenu = self.menuBar.addMenu('&View')
measureMenu = self.menuBar.addMenu('&Measure')
helpMenu = self.menuBar.addMenu('&Help')
readZmatAction = QAction('&Read &ZMat', self)
readZmatAction.setShortcut('Ctrl+O')
readZmatAction.setStatusTip('Read Zmat from file')
readZmatAction.triggered.connect(self.readZmat)
fileMenu.addAction(readZmatAction)
readXYZAction = QAction('&Read &XYZ', self)
readXYZAction.setShortcut('Ctrl+Shift+O')
readXYZAction.setStatusTip('Read XYZ from file')
readXYZAction.triggered.connect(self.readXYZ)
fileMenu.addAction(readXYZAction)
readGaussianAction = QAction('&Read &Gaussian log', self)
readGaussianAction.setShortcut('Ctrl+G')
readGaussianAction.setStatusTip('Read Gaussian log file')
readGaussianAction.triggered.connect(self.readGaussian)
fileMenu.addAction(readGaussianAction)
writeZmatAction = QAction('&Write &ZMat', self)
writeZmatAction.setShortcut('Ctrl+S')
writeZmatAction.setStatusTip('Write Zmat to file')
writeZmatAction.triggered.connect(self.writeZmat)
fileMenu.addAction(writeZmatAction)
writeXYZAction = QAction('&Write &XYZ', self)
writeXYZAction.setShortcut('Ctrl+Shift+S')
writeXYZAction.setStatusTip('Write XYZ from file')
writeXYZAction.triggered.connect(self.writeXYZ)
fileMenu.addAction(writeXYZAction)
exitAction = QAction('&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit application')
exitAction.triggered.connect(qApp.quit)
fileMenu.addAction(exitAction)
addRowAction = QAction('&Add &row', self)
addRowAction.setShortcut('Ctrl+R')
addRowAction.setStatusTip('Add row to ZMatrix')
addRowAction.triggered.connect(self.addRow)
editMenu.addAction(addRowAction)
deleteRowAction = QAction('&Delete &row', self)
deleteRowAction.setShortcut('Ctrl+Shift+R')
deleteRowAction.setStatusTip('Delete row from ZMatrix')
deleteRowAction.triggered.connect(self.deleteRow)
editMenu.addAction(deleteRowAction)
addAtomAction = QAction('&Add &atom', self)
addAtomAction.setShortcut('Ctrl+A')
addAtomAction.setStatusTip('Add atom to ZMatrix')
addAtomAction.triggered.connect(self.buildB)
editMenu.addAction(addAtomAction)
drawModeMenu = QMenu('Draw mode', self)
viewMenu.addMenu(drawModeMenu)
fastDrawAction = QAction('&Fast draw', self)
fastDrawAction.triggered.connect(self.fastDraw)
normalDrawAction = QAction('&Normal draw', self)
normalDrawAction.triggered.connect(self.normalDraw)
drawModeMenu.addAction(normalDrawAction)
drawModeMenu.addAction(fastDrawAction)
clearHighlightsAction = QAction('&Clear selection', self)
clearHighlightsAction.setShortcut('Ctrl+C')
clearHighlightsAction.setStatusTip('Clear highlighted atoms')
clearHighlightsAction.triggered.connect(self.clearHighlights)
viewMenu.addAction(clearHighlightsAction)
clearLabelsAction = QAction('&Clear labels', self)
clearLabelsAction.setShortcut('Ctrl+Alt+C')
clearLabelsAction.setStatusTip('Clear labels')
clearLabelsAction.triggered.connect(self.clearLabels)
viewMenu.addAction(clearLabelsAction)
clearUpdateViewAction = QAction('&Clear selection and labels', self)
clearUpdateViewAction.setShortcut('Ctrl+Shift+C')
clearUpdateViewAction.setStatusTip('Clear highlighted atoms and labels')
clearUpdateViewAction.triggered.connect(self.clearUpdateView)
viewMenu.addAction(clearUpdateViewAction)
self.showGaussAction = QAction('Show &Gaussian geometry optimization', self)
self.showGaussAction.setShortcut('Ctrl+G')
self.showGaussAction.setStatusTip('Show Gaussian geometry optimization plots for energy, force and displacement.')
self.showGaussAction.setEnabled(False)
self.showGaussAction.triggered.connect(self.showGauss)
viewMenu.addAction(self.showGaussAction)
self.showFreqAction = QAction('Show &IR frequency plot', self)
self.showFreqAction.setShortcut('Ctrl+I')
self.showFreqAction.setStatusTip('Show Gaussian calculated IR frequency plot.')
self.showFreqAction.setEnabled(False)
self.showFreqAction.triggered.connect(self.showFreq)
viewMenu.addAction(self.showFreqAction)
measureDistanceAction = QAction('&Measure &distance', self)
measureDistanceAction.setShortcut('Ctrl+D')
measureDistanceAction.setStatusTip('Measure distance between two atoms')
measureDistanceAction.triggered.connect(self.measureDistanceB)
measureMenu.addAction(measureDistanceAction)
measureAngleAction = QAction('&Measure &angle', self)
measureAngleAction.setShortcut('Ctrl+Shift+D')
measureAngleAction.setStatusTip('Measure angle between three atoms')
measureAngleAction.triggered.connect(self.measureAngleB)
measureMenu.addAction(measureAngleAction)
aboutAction = QAction('&About', self)
aboutAction.setStatusTip('About this program...')
aboutAction.triggered.connect(self.about)
helpMenu.addAction(aboutAction)
aboutQtAction = QAction('&About Qt', self)
aboutQtAction.setStatusTip('About Qt...')
aboutQtAction.triggered.connect(self.aboutQt)
helpMenu.addAction(aboutQtAction)
# define GL widget that displays the 3D molecule model
self.window = widgets.MyGLView()
self.window.installEventFilter(self)
self.window.setMinimumSize(500, 500)
#self.window.setBackgroundColor((50, 0, 10))
self.updateView()
self.gaussianPlot = GraphicsLayoutWidget()
self.gaussianPlot.resize(750, 250)
self.gaussianPlot.setWindowTitle('Gaussian geometry optimization')
#self.gaussianPlot.setAspectLocked(True)
#self.gaussianPlot.addLayout(rowspan=3, colspan=1)
self.FreqModel = QStandardItemModel(1, 3, self)
self.freqTable = QTableView(self)
self.freqTable.setModel(self.FreqModel)
self.freqTable.setMinimumWidth(240)
self.freqTable.installEventFilter(self)
self.FreqModel.installEventFilter(self)
self.FreqModel.setHorizontalHeaderLabels(['Frequency','IR Intensity','Raman Intensity'])
for j, width in enumerate([80, 80, 80]):
self.freqTable.setColumnWidth(j, width)
self.freqWidget = QWidget()
self.freqWidget.setWindowTitle('IR frequency plot & table')
self.freqWidget.resize(800, 400)
self.freqWidget.layout = QHBoxLayout(self.freqWidget)
self.freqWidget.layout.setSpacing(1)
self.freqWidget.layout.setContentsMargins(1, 1, 1, 1)
self.freqPlot = GraphicsLayoutWidget()
self.freqWidget.layout.addWidget(self.freqPlot)
self.freqWidget.layout.addWidget(self.freqTable)
self.freqTable.clicked.connect(self.freqCellClicked)
# define other application parts
self.statusBar = QStatusBar(self)
self.fileDialog = QFileDialog(self)
# define application layout
self.layout = QVBoxLayout(self)
self.layout.setSpacing(1)
self.layout.setContentsMargins(1, 1, 1, 1)
self.layout1 = QHBoxLayout()
self.layout1.setSpacing(1)
self.layout1.addWidget(self.ZMatTable)
self.layout1.addWidget(self.window)
self.layout.addWidget(self.menuBar)
self.layout.addLayout(self.layout1)
self.layout.addWidget(self.statusBar)
self.adjustSize()
self.setWindowTitle('Moldy')
iconPath = 'icon.png'
icon = QIcon(iconPath)
icon.addFile(iconPath, QSize(16, 16))
icon.addFile(iconPath, QSize(24, 24))
icon.addFile(iconPath, QSize(32, 32))
icon.addFile(iconPath, QSize(48, 48))
icon.addFile(iconPath, QSize(256, 256))
self.setWindowIcon(icon)
# start monitoring changes in the ZMatModel
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
# run and show the application
def run(self):
self.show()
self.ZMatTable.clicked.connect(self.ZMatCellClicked)
qt_app.instance().aboutToQuit.connect(self.deleteGLwidget)
qt_app.exec_()
# fill the ZMatModel with initial data from 'self.inp'
def populateZMatModel(self):
self.ZMatModel.removeRows(0, self.ZMatModel.rowCount())
for i, row in enumerate(self.inp):
for j, cell in enumerate(row):
item = QStandardItem(str(cell))
self.ZMatModel.setItem(i, j, item)
# some cells should not be editable, they are disabled
for i in range(min(len(self.inp), 3)):
for j in range(2*i+1, 7):
self.ZMatModel.setItem(i, j, QStandardItem())
self.ZMatModel.item(i, j).setBackground(QColor(150,150,150))
self.ZMatModel.item(i, j).setFlags(Qt.ItemIsEnabled)
def populateFreqModel(self):
self.FreqModel.removeRows(0, self.FreqModel.rowCount())
for i, row in enumerate(zip(self.vibfreqs, self.vibirs, self.vibramans)):
for j, cell in enumerate(row):
item = QStandardItem(str(cell))
self.FreqModel.setItem(i, j, item)
# add a row to the bottom of the ZMatModel
def addRow(self):
# temporarily stop updating the GL window
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
row = self.ZMatModel.rowCount()
self.ZMatModel.insertRow(row)
# some cells should not be editable
if row < 3:
for j in range(2*row+1, 7):
self.ZMatModel.setItem(row, j, QStandardItem())
self.ZMatModel.item(row, j).setBackground(QColor(150,150,150))
self.ZMatModel.item(row, j).setFlags(Qt.ItemIsEnabled)
# restart GL window updating
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.statusBar.clearMessage()
self.statusBar.showMessage('Added 1 row.', 3000)
# delete the last row of the ZMatModel
def deleteRow(self):
xyz = [list(vi) for vi in list(v)]
atoms = [str(elements[e]) for e in elems]
oldLen = self.ZMatModel.rowCount()
idxs = sorted(set(idx.row() for idx in self.ZMatTable.selectedIndexes()), reverse=True)
newLen = oldLen - len(idxs)
if newLen == oldLen:
self.ZMatModel.removeRow(self.ZMatModel.rowCount()-1)
else:
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
for idx in idxs:
self.ZMatModel.removeRow(idx)
if idx < 3:
for i in range(idx, min(3, newLen)):
for j in range(2*i+1, 7):
self.ZMatModel.setItem(i, j, QStandardItem())
self.ZMatModel.item(i, j).setBackground(QColor(150,150,150))
self.ZMatModel.item(i, j).setFlags(Qt.ItemIsEnabled)
if len(xyz) > idx:
xyz.pop(idx)
atoms.pop(idx)
self.inp = xyz2zmat(xyz, atoms)
self.populateZMatModel()
for i in reversed(self.highList):
self.window.removeItem(i[1])
self.highList = []
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
self.statusBar.clearMessage()
if idxs:
self.statusBar.showMessage('Deleted row(s): '+str([i+1 for i in idxs]), 3000)
else:
self.statusBar.showMessage('Deleted last row.', 3000)
# show the periodic table widget
def periodicTable(self):
self.statusBar.clearMessage()
self.statusBar.showMessage('Select element from periodic table.')
self.periodicTableWidget.exec_()
selection = self.periodicTableWidget.selection()
return selection
# import molecule with zmatrix coordinates
def readZmat(self):
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
filename = self.fileDialog.getOpenFileName(self, 'Open file', expanduser('~'), '*.zmat;;*.*')
self.inp = []
self.populateZMatModel()
if filename:
with open(filename, 'r') as f:
next(f)
next(f)
for row in f:
self.inp.append(row.split())
f.close()
self.populateZMatModel()
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
self.statusBar.clearMessage()
self.statusBar.showMessage('Read molecule from '+filename+'.', 5000)
self.showGaussAction.setEnabled(False)
self.showFreqAction.setEnabled(False)
# import molecule with xyz coordinates
def readXYZ(self):
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
filename = self.fileDialog.getOpenFileName(self, 'Open file', expanduser('~'), '*.xyz;;*.*')
xyz = []
elems = []
self.inp = []
self.populateZMatModel()
if filename:
with open(filename, 'r') as f:
next(f)
next(f)
for row in f:
rs = row.split()
if len(rs) == 4:
elems.append(rs[0])
xyz.append([float(f) for f in rs[1:]])
f.close()
self.inp = xyz2zmat(xyz, elems)
self.populateZMatModel()
#print(elems)
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
self.statusBar.clearMessage()
self.statusBar.showMessage('Read molecule from '+filename+'.', 5000)
self.showGaussAction.setEnabled(False)
self.showFreqAction.setEnabled(False)
# import Gaussian log file
def readGaussian(self):
global vsShifted
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
filename = self.fileDialog.getOpenFileName(self, 'Open file', expanduser('~'), '*.log;;*.*')
if filename:
self.gaussianPlot.clear()
self.inp = []
self.populateZMatModel()
file = ccopen(filename)
data = file.parse().getattributes()
self.natom = data['natom']
self.atomnos = data['atomnos'].tolist()
self.atomsymbols = [ str(elements[e]) for e in self.atomnos ]
self.atomcoords = data['atomcoords'].tolist()
self.scfenergies = data['scfenergies'].tolist()
self.geovalues = data['geovalues'].T.tolist()
self.geotargets = data['geotargets'].tolist()
if 'vibfreqs' in data.keys():
self.vibfreqs = data['vibfreqs']
#print(self.vibfreqs)
self.vibirs = data['vibirs']
#print(self.vibirs)
#print(data.keys())
if 'vibramans' in data.keys():
self.vibramans = data['vibramans']
else:
self.vibramans = [''] * len(self.vibirs)
self.vibdisps = data['vibdisps']
#print(self.vibdisps)
self.inp = xyz2zmat(self.atomcoords[0], self.atomsymbols)
self.populateZMatModel()
titles = ['SCF Energies', 'RMS & Max Forces', 'RMS & Max Displacements']
for i in range(3):
self.gaussianPlot.addPlot(row=1, col=i+1)
plot = self.gaussianPlot.getItem(1, i+1)
plot.setTitle(title=titles[i])
if i == 0:
c = ['c']
x = [0]
y = [self.scfenergies]
else:
c = ['r', 'y']
x = [0, 0]
y = [self.geovalues[2*i-2], self.geovalues[2*i-1]]
targety = [self.geotargets[2*i-2], self.geotargets[2*i-1]]
plot.clear()
plot.maxData = plot.plot(y[0], symbol='o', symbolPen=c[0], symbolBrush=c[0], pen=c[0], symbolSize=5, pxMode=True, antialias=True, autoDownsample=False)
plot.highlight=plot.plot(x, [ yy[0] for yy in y ], symbol='o', symbolPen='w', symbolBrush=None, pen=None, symbolSize=15, pxMode=True, antialias=True, autoDownsample=False)
plot.maxData.sigPointsClicked.connect(self.gausclicked)
if i > 0:
for j in range(2):
plot.addLine(y=np.log10(targety[j]), pen=mkPen((255, 255*j, 0, int(255/2)), width=1))
plot.RMSData=plot.plot(y[1], symbol='o', symbolPen=c[1], symbolBrush=c[1], pen=c[1], symbolSize=5, pxMode=True, antialias=True, autoDownsample=False)
plot.RMSData.sigPointsClicked.connect(self.gausclicked)
plot.setLogMode(y=True)
self.showGauss()
self.updateView()
self.statusBar.clearMessage()
self.statusBar.showMessage('Read molecule from '+filename+'.', 5000)
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
if self.natom:
self.showGaussAction.setEnabled(True)
if 'vibfreqs' in data.keys():
self.showFreqAction.setEnabled(True)
# populate the FreqModel
self.populateFreqModel()
self.freqPlot.clear()
irPlot = self.freqPlot.addPlot(row=1, col=1)
irPlot.clear()
minFreq = np.min(self.vibfreqs)
maxFreq = np.max(self.vibfreqs)
maxInt = np.max(self.vibirs)
x = np.sort(np.concatenate([np.linspace(minFreq-100, maxFreq+100, num=1000), self.vibfreqs]))
y = x*0
for f,i in zip(self.vibfreqs, self.vibirs):
y += lorentzv(x, f, 2*np.pi, i)
#xy = np.array([np.concatenate([x, np.array(self.vibfreqs)]), np.concatenate([y, np.array(self.vibirs)])]).T
#xysort = xy[xy[:,0].argsort()]
irPlot.maxData = irPlot.plot(x, y, antialias=True)
markers = ErrorBarItem(x=self.vibfreqs, y=self.vibirs, top=maxInt/30, bottom=None, pen='r')
irPlot.addItem(markers)
self.showFreq()
#self.vibdisps = np.append(self.vibdisps, [np.mean(self.vibdisps, axis=0)], axis=0)
maxt = 100
vsShifted = np.array([ [ vs + self.vibdisps[i]*np.sin(t*2*np.pi/maxt)/3 for t in range(maxt) ] for i in range(len(self.vibfreqs)) ])
else:
self.showFreqAction.setEnabled(False)
self.freqWidget.hide()
def showGauss(self):
self.gaussianPlot.show()
def showFreq(self):
self.freqWidget.show()
# export Zmatrix to csv
def writeZmat(self):
zm = model2list(self.ZMatModel)
filename = self.fileDialog.getSaveFileName(self, 'Save file', expanduser('~')+'/'+getFormula(list(list(zip(*zm))[0]))+'.zmat', '*.zmat;;*.*')
try:
filename
except NameError:
pass
else:
if filename:
writeOutput(zm, filename)
self.statusBar.clearMessage()
self.statusBar.showMessage('Wrote molecule to '+filename+'.', 5000)
# export XYZ coordinates to csv
def writeXYZ(self):
xyz = []
zm = model2list(self.ZMatModel)
for i in range(len(v)):
xyz.append(np.round(v[i], 7).tolist())
xyz[i][:0] = zm[i][0]
if len(v) > 0:
formula = getFormula(list(list(zip(*xyz))[0]))
else:
formula = 'moldy_output'
filename = self.fileDialog.getSaveFileName(self, 'Save file', expanduser('~')+'/'+formula+'.xyz', '*.xyz;;*.*')
try:
filename
except NameError:
pass
else:
if filename:
writeOutput(xyz, filename)
self.statusBar.clearMessage()
self.statusBar.showMessage('Wrote molecule to '+filename+'.', 5000)
# redraw the 3D molecule in GL widget
def updateView(self):
global r
global c
global v
global vs
global elems
global nelems
data = model2list(self.ZMatModel)
try:
# create a list with element coordinates
v = zmat2xyz(data)
except (AssertionError, IndexError, ZMError):
pass
else:
# clear the screen before redraw
for item in reversed(self.window.items):
self.window.removeItem(item)
# create a second coordinate list 'vs' that is centered in the GL view
self.atomList = []
if len(v) > 0:
shift = np.mean(v, axis=0)
vs = np.add(v, -shift)
elems = [ 1 + next((i for i, sublist in enumerate(colors) if row[0] in sublist), -1) for row in data ]
nelems = len(elems)
# define molecule radii and colors
r = []
c = []
for i in elems:
r.append(elements[i].covalent_radius)
c.append(colors[i-1][-1])
# draw atoms
for i in range(nelems):
addAtom(self.window, i, r, vs, c, fast=self.fast)
self.atomList.append([i, self.window.items[-1]])
#print(self.atomList)
# draw bonds where appropriate
combs = list(itertools.combinations(range(nelems), 2))
bonds = []
for i in combs:
bonds.append(addBond(self.window, i[0], i[1], r, vs, c, fast=self.fast))
if self.fast:
bondedAtoms = set(filter((None).__ne__, flatten(bonds)))
for i in set(range(nelems)) - bondedAtoms:
addUnbonded(self.window, i, vs, c)
self.atomList[i][1]=self.window.items[-1]
#print(self.atomList)
for i in self.highList:
self.window.addItem(i[1])
for i in self.labelList:
self.window.addItem(i)
if len(v) > 1:
maxDim = float('-inf')
for dim in v.T:
span = max(dim)-min(dim)
if span > maxDim:
maxDim = span
else: maxDim = 2
self.window.setCameraPosition(distance=maxDim*1.5+1)
global index
index = 0
def updateFreq(self):
global vsShifted, index, r, c
index += 1
index = index % len(vsShifted[0])
#print(index)
#print(vsShifted[index])
for item in reversed(self.window.items):
self.window.removeItem(item)
for i in range(nelems):
addAtom(self.window, i, r, vsShifted[self.freqIndex, index], c, fast=self.fast)
self.atomList.append([i, self.window.items[-1]])
combs = itertools.combinations(range(nelems), 2)
bonds = []
for i in combs:
bonds.append(addBond(self.window, i[0], i[1], r, vsShifted[self.freqIndex, index], c, fast=self.fast))
if self.fast:
bondedAtoms = set(filter((None).__ne__, flatten(bonds)))
for i in set(range(nelems)) - bondedAtoms:
addUnbonded(self.window, i, vsShifted[self.freqIndex, index], c)
self.atomList[i][1]=self.window.items[-1]
# detect mouse clicks in GL window and process them
def eventFilter(self, obj, event):
if obj == self.window:
if event.type() == event.MouseButtonPress:
itms = obj.itemsAt((event.pos().x()-2, event.pos().y()-2, 4, 4))
if len(itms):
self.highlight(obj, [itms[0]])
elif len(self.atomList) == 0:
self.build()
# also do the default click action
return super(MainWidget, self).eventFilter(obj, event)
def ZMatCellClicked(self):
idxs = sorted(set(idx.row() for idx in self.ZMatTable.selectedIndexes()), reverse=True)
itms = []
if self.highList:
highIdx = list(np.array(self.highList).T[0])
for idx in idxs:
if self.highList and idx in highIdx:
itms.append(self.highList[highIdx.index(idx)][1])
elif len(self.atomList) > idx:
itms.append(self.atomList[idx][1])
self.highlight(self.window, itms)
def freqCellClicked(self):
global vsShifted
self.timer = QTimer()
self.timer.setInterval(30)
self.timer.timeout.connect(self.updateFreq)
idxs = [ idx.row() for idx in self.freqTable.selectedIndexes() ]
if len(idxs) == 1:
self.freqIndex = idxs[0]
self.timer.stop()
self.timer.timeout.connect(self.updateFreq)
try:
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
except TypeError:
pass
self.timer.start()
if len(idxs) != 1:
self.timer.stop()
self.freqTable.clearSelection()
self.timer.timeout.disconnect(self.updateFreq)
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.clearUpdateView()
def gausclicked(self, item, point):
itemdata = item.scatter.data
points = [ row[7] for row in itemdata ]
idx = points.index(point[0])
for i in range(3):
if i == 0:
x = [idx]
y = [self.scfenergies[idx]]
else:
x = [idx, idx]
y = [self.geovalues[2*i-2][idx], self.geovalues[2*i-1][idx]]
plot = self.gaussianPlot.getItem(1, i+1)
plot.removeItem(plot.highlight)
plot.highlight=plot.plot(x, y, symbol='o', symbolPen='w', symbolBrush=None, pen=None, symbolSize=15, pxMode=True, antialias=True, autoDownsample=False)
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
self.inp = []
self.populateZMatModel()
self.inp = xyz2zmat(self.atomcoords[min(idx, len(self.atomcoords)-1)], self.atomsymbols)
self.populateZMatModel()
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
def highlight(self, obj, itms):
for itm in itms:
idx = next((i for i, sublist in enumerate(self.atomList) if itm in sublist), -1)
#print(idx)
if idx != -1:
addAtom(obj, idx, r, vs, c, opt='highlight', fast=self.fast)
self.highList.append([idx, obj.items[-1]])
self.ZMatTable.selectRow(idx)
idx = next((i for i, sublist in enumerate(self.highList) if itm in sublist), -1)
if idx != -1:
obj.removeItem(self.highList[idx][1])
self.highList.pop(idx)
self.ZMatTable.clearSelection()
self.statusBar.clearMessage()
if len(self.highList) > 0:
idxs = np.asarray(self.highList).T[0]
selected = []
for i in idxs:
selected.append(str(i+1)+str(elements[elems[i]]))
self.statusBar.showMessage('Selected atoms: '+str(selected), 5000)
def buildB(self):
try:
nelems
except NameError:
self.build()
else:
if len(self.highList) <= min(nelems, 3):
diff = min(nelems, 3) - len(self.highList)
if diff != 0:
self.statusBar.clearMessage()
self.statusBar.showMessage('Please select '+str(diff)+' more atom(s).')
else:
self.build()
else:
self.statusBar.clearMessage()
self.statusBar.showMessage('Too many atoms selected.')
def build(self):
selection = self.periodicTable()
row = self.ZMatModel.rowCount()
self.addRow()
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
newSymbol = selection[1]
newData = [newSymbol]
if len(self.highList) >= 1:
newBond = round(2.1*gmean([ elements[e].covalent_radius for e in [selection[0], elems[self.highList[0][0]]] ]), 4)
newData.append(self.highList[0][0]+1)
newData.append(newBond)
if len(self.highList) >= 2:
newAngle = 109.4712
newData.append(self.highList[1][0]+1)
newData.append(newAngle)
if len(self.highList) == 3:
newDihedral = 120.
newData.append(self.highList[2][0]+1)
newData.append(newDihedral)
for j, cell in enumerate(newData):
item = QStandardItem(str(cell))
self.ZMatModel.setItem(row, j, item)
self.highList = []
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
def measureDistanceB(self):
sel = len(self.highList)
if sel <= 2:
if sel < 2:
self.statusBar.clearMessage()
self.statusBar.showMessage('Please select '+str(2-sel)+' more atom(s).')
else:
self.measureDistance()
else:
self.statusBar.clearMessage()
self.statusBar.showMessage('Too many atoms selected.')
def measureDistance(self):
pts = []
for pt in self.highList:
pts.append(vs[pt[0]])
pts = np.array(pts)
self.clearHighlights()
line = gl.GLLinePlotItem(pos=pts, color=(0., 1., 0., 1.), width=3)
self.window.addItem(line)
self.labelList.append(line)
q = pts[1]-pts[0]
dist = round(np.sqrt(np.dot(q, q)), 4)
self.window.labelPos.append(np.mean(pts[0:2], axis=0))
self.window.labelText.append(str(dist))
self.statusBar.clearMessage()
self.statusBar.showMessage('Measured distance: '+str(dist)+' A.', 3000)
def measureAngleB(self):
sel = len(self.highList)
if sel <= 3:
if sel < 3:
self.statusBar.clearMessage()
self.statusBar.showMessage('Please select '+str(3-sel)+' more atom(s).')
else:
self.measureAngle()
else:
self.statusBar.clearMessage()
self.statusBar.showMessage('Too many atoms selected.')
def measureAngle(self):
pts = []
for pt in self.highList:
pts.append(vs[pt[0]])
pts = np.array(pts)
q = pts[1]-pts[0]
r = pts[2]-pts[0]
q_u = q / np.sqrt(np.dot(q, q))
r_u = r / np.sqrt(np.dot(r, r))
angle = round(degrees(acos(np.dot(q_u, r_u))), 1)
srange = np.array([slerp(q, r, t) for t in np.arange(0.0, 13/12, 1/12)])
self.clearHighlights()
for i in range(12):
mesh = gl.MeshData(np.array([[0,0,0],srange[i],srange[i+1]]))
tri = gl.GLMeshItem(meshdata=mesh, smooth=False, computeNormals=False, color=(0.3, 1., 0.3, 0.5), glOptions=('translucent'))
tri.translate(pts[0][0], pts[0][1], pts[0][2])
self.window.addItem(tri)
self.labelList.append(tri)
self.window.labelPos.append(slerp(q, r, 0.5)+pts[0])
self.window.labelText.append(str(angle))
self.statusBar.clearMessage()
self.statusBar.showMessage('Measured angle: '+str(angle)+'°', 3000)
def clearLabels(self):
self.window.labelPos = []
self.window.labelText = []
self.labelList = []
self.updateView()
def clearHighlights(self):
for item in reversed(self.highList):
self.window.removeItem(item[1])
self.highList = []
self.updateView()
def clearUpdateView(self):
self.window.labelPos = []
self.window.labelText = []
self.labelList = []
for item in reversed(self.highList):
self.window.removeItem(item[1])
self.highList = []
self.updateView()
#print(self.highList)
def fastDraw(self):
if not self.fast:
self.fast = True
self.updateView()
def normalDraw(self):
if self.fast:
self.fast = False
self.updateView()
def about(self):
QMessageBox.about(self, 'About moldy', 'moldy beta 15. 9. 2015')
def aboutQt(self):
QMessageBox.aboutQt(self, 'About Qt')
def deleteGLwidget(self):
self.window.setParent(None)
del self.window
def SaveAction(self):
#Filename zum Speichern vom Benutzer erfragen
filename = QFileDialog.getSaveFileName(self, 'Messung Speichern')
if not filename == '':
self.MainProgramm.SaveFile(filename)
def ExportAction(self):
filename = QFileDialog.getSaveFileName(self, 'Messung Exportieren')
if not filename == '':
self.MainProgramm.Export(filename)
return
def saveToFileBowditch(self):
''' the bowditch needs to be setup such that the final coordinate is a known point, a single letter, then the reference
will be in the next 2 rows, with a dash next to the single letter'''
fileName = QFileDialog.getSaveFileName(self, "Open Points File", "",
"Excel (*.xlsx)", "")
dX, dY = bowditchAdjust(self.provisionals, self.control,
self.obsOrder[-1][4:])
self.bowditch.setText("not completed yet.")
sumDistance = 0
for i, j in self.obs1.iteritems():
for p, t in j.iteritems():
if self.provisionals.has_key(p):
sumDistance = sumDistance + t.distance
dX = dX / sumDistance
dY = dY / sumDistance
fileName = str(fileName)
workbook = xlsxwriter.Workbook(fileName)
worksheet = workbook.add_worksheet()
i = 0
worksheet.write(0, 0, 'Leg')
worksheet.write(0, 1, 'Dir/OrCorr./Dis')
worksheet.write(0, 2, 'Name')
worksheet.write(0, 3, 'Y')
worksheet.write(0, 4, 'X')
worksheet.write(2, 2, self.control[self.stationsOrder[0]].name)
worksheet.write(2, 3, self.control[self.stationsOrder[0]].y)
worksheet.write(2, 4, self.control[self.stationsOrder[0]].x)
i += 4
temp = self.stationsOrder[0]
soFar = 0
format = workbook.add_format()
format.set_underline()
for nm3 in self.stationsOrder:
for nm, ob in self.obs1[nm3].iteritems():
if self.provisionals.has_key(nm):
worksheet.write(i, 0, nm3 + "-" + nm)
worksheet.write(i, 1,
rad2dms(self.obs1[nm3][nm].direction))
worksheet.write(i, 2, nm)
worksheet.write(i, 3, round(self.provisionals[nm].y, 3))
worksheet.write(i, 4, round(self.provisionals[nm].x, 3))
i += 1
ldist = self.obs1[nm3][nm].distance
soFar += ldist
worksheet.write(i, 3, soFar * dY)
worksheet.write(i, 4, soFar * dX)
i += 1
worksheet.write(
i, 1,
str(round(self.obs1[nm3][nm].distance, 2)) + "m")
worksheet.write(i, 2, nm, format)
worksheet.write(
i, 3, round(self.provisionals[nm].y + soFar * dY, 2),
format)
worksheet.write(
i, 4, round(self.provisionals[nm].x + soFar * dX, 2),
format)
i += 2
temp = nm
workbook.close()
def writeOut(self):
fileName = QFileDialog.getSaveFileName(self, "Open Points File", "",
"Text File (*.txt);;", "")
file = open(fileName, "w")
file.write("________CONTROL POINTS________\n\n")
for i, j in self.control.iteritems():
file.write(i + ":\n" + str(j) + "\n")
file.write("________UNKNOWNS________\n\n")
file.write(str(self.unknowns) + '\n\n')
file.write(
"_______________________________________ CALCULATIONS _______________________________________ \n\n\n\n"
)
k = 0
for i in range(self.iterations):
k += 1
provis = adjustProvisional(self.Xdict, self.provis, self.obs,
self.unknowns)
A, Xdict, provis, obs, control, unknowns, L = Iterate(
provis, self.obs, self.control, self.unknowns, self.P)
X = ((A.T * self.P * A)**-1) * A.T * self.P * L
Xdict = Points("Solutions Dictionary")
j = 0
for i in unknowns:
Xdict[i] = X[j]
j += 1
V, posteriori, covarience_mat, precisi = precisions(
A, X, self.P, L, obs, unknowns)
file.write("________ITERATION: " + str(k) + " ________\n\n")
if float(round(float((A.T * self.P * V).T * (A.T * self.P * V)),
6)) == 0.:
file.write(
"____________________________________________________\n\nCalculation check 'A.tPV' successful\n---------------------------------------------\n"
)
else:
file.write(
"Calculation check 'A.tPV' unsuccessful to 6 dec places\n\n"
)
# V,posteriori,covarience_mat,precisions
file.write("________'V.TPV'________\n\n")
file.write(str(V.T * self.P * V) + '\n\n')
file.write("________Posteriori________\n\n")
file.write(str(posteriori) + '\n\n')
# file.write("________Covarience Matrix________\n\n") # COVARIENCE MATRIX
# file.write(str(covarience_mat)+'\n\n')
file.write("________Precisions of Unknowns ________\n\n")
for i, j in precisi.iteritems():
file.write(i + ":\n" + str(round(float(j), 3)) + "\n\n")
check = globalCheck(provis, control, V, obs, unknowns, Xdict)
file.write("________Global Check________\n\n")
for i, j in check.iteritems():
file.write(i + ":\n" + str(j) + "\n")
file.write("________________---- END OF ITERATION " + str(k) +
" ----____________\n\n")
file.write(
"_______________________________________________________________________\n\n"
)
# showGraph(N,provisionals,control)
file.write("________FINAL COORDINATES________\n\n")
for i, j in provis.iteritems():
file.write(i + ":\n" + str(j) + "\n\n")
file.write(
"________X Solution Vector, With distances in meters and directions in seconds ________\n\n"
)
for i, j in Xdict.iteritems():
file.write(i + ":\n" + str(round(float(j), 3)) + "\n\n")
def ExportAction(self):
filename = QFileDialog.getSaveFileName(self, 'Messung Exportieren')
if not filename == '':
self.MainProgramm.Export(filename)
return
def __init__(self,
title=_('Choose Files'),
filters=[],
add_all_files_filter=True,
parent=None,
modal=True,
name='',
mode=QFileDialog.ExistingFiles,
default_dir='~'):
QObject.__init__(self)
ftext = ''
if filters:
for filter in filters:
text, extensions = filter
extensions = [
'*' + (i if i.startswith('.') else '.' + i)
for i in extensions
]
ftext += '%s (%s);;' % (text, ' '.join(extensions))
if add_all_files_filter or not ftext:
ftext += 'All files (*)'
if ftext.endswith(';;'):
ftext = ftext[:-2]
self.dialog_name = name if name else 'dialog_' + title
self.selected_files = None
self.fd = None
initial_dir = dynamic.get(self.dialog_name,
os.path.expanduser(default_dir))
if not isinstance(initial_dir, basestring):
initial_dir = os.path.expanduser(default_dir)
self.selected_files = []
with SanitizeLibraryPath():
if mode == QFileDialog.AnyFile:
f = unicode(
QFileDialog.getSaveFileName(parent, title, initial_dir,
ftext, ""))
if f:
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFile:
f = unicode(
QFileDialog.getOpenFileName(parent, title, initial_dir,
ftext, ""))
if f and os.path.exists(f):
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFiles:
fs = QFileDialog.getOpenFileNames(parent, title, initial_dir,
ftext, "")
for f in fs:
f = unicode(f)
if not f: continue
if not os.path.exists(f):
# QFileDialog for some reason quotes spaces
# on linux if there is more than one space in a row
f = unquote(f)
if f and os.path.exists(f):
self.selected_files.append(f)
else:
opts = QFileDialog.ShowDirsOnly if mode == QFileDialog.Directory else QFileDialog.Option(
)
f = unicode(
QFileDialog.getExistingDirectory(parent, title,
initial_dir, opts))
if os.path.exists(f):
self.selected_files.append(f)
if self.selected_files:
self.selected_files = [unicode(q) for q in self.selected_files]
saved_loc = self.selected_files[0]
if os.path.isfile(saved_loc):
saved_loc = os.path.dirname(saved_loc)
dynamic[self.dialog_name] = saved_loc
self.accepted = bool(self.selected_files)
def __init__(
self,
title=_("Choose Files"),
filters=[],
add_all_files_filter=True,
parent=None,
modal=True,
name="",
mode=QFileDialog.ExistingFiles,
default_dir="~",
no_save_dir=False,
):
QObject.__init__(self)
ftext = ""
if filters:
for filter in filters:
text, extensions = filter
extensions = ["*" + (i if i.startswith(".") else "." + i) for i in extensions]
ftext += "%s (%s);;" % (text, " ".join(extensions))
if add_all_files_filter or not ftext:
ftext += "All files (*)"
if ftext.endswith(";;"):
ftext = ftext[:-2]
self.dialog_name = name if name else "dialog_" + title
self.selected_files = None
self.fd = None
if no_save_dir:
initial_dir = os.path.expanduser(default_dir)
else:
initial_dir = dynamic.get(self.dialog_name, os.path.expanduser(default_dir))
if not isinstance(initial_dir, basestring):
initial_dir = os.path.expanduser(default_dir)
self.selected_files = []
use_native_dialog = "CALIBRE_NO_NATIVE_FILEDIALOGS" not in os.environ
with SanitizeLibraryPath():
opts = QFileDialog.Option()
if not use_native_dialog:
opts |= QFileDialog.DontUseNativeDialog
if mode == QFileDialog.AnyFile:
f = unicode(QFileDialog.getSaveFileName(parent, title, initial_dir, ftext, "", opts))
if f:
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFile:
f = unicode(QFileDialog.getOpenFileName(parent, title, initial_dir, ftext, "", opts))
if f and os.path.exists(f):
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFiles:
fs = QFileDialog.getOpenFileNames(parent, title, initial_dir, ftext, "", opts)
for f in fs:
f = unicode(f)
if not f:
continue
if not os.path.exists(f):
# QFileDialog for some reason quotes spaces
# on linux if there is more than one space in a row
f = unquote(f)
if f and os.path.exists(f):
self.selected_files.append(f)
else:
if mode == QFileDialog.Directory:
opts |= QFileDialog.ShowDirsOnly
f = unicode(QFileDialog.getExistingDirectory(parent, title, initial_dir, opts))
if os.path.exists(f):
self.selected_files.append(f)
if self.selected_files:
self.selected_files = [unicode(q) for q in self.selected_files]
saved_loc = self.selected_files[0]
if os.path.isfile(saved_loc):
saved_loc = os.path.dirname(saved_loc)
if not no_save_dir:
dynamic[self.dialog_name] = saved_loc
self.accepted = bool(self.selected_files)
def fileSaveMovie(self):
"""
Save a copy of the current movie file loaded in the Movie Player.
"""
# Make sure there is a moviefile to save.
if not self.w.assy.current_movie or not self.w.assy.current_movie.filename \
or not os.path.exists(self.w.assy.current_movie.filename):
msg = redmsg("Save Movie File: No movie file to save.")
env.history.message(msg)
msg = "To create a movie, click on the <b>Simulator</b> <img source=\"simicon\"> icon."
#QMimeSourceFactory.defaultFactory().setPixmap( "simicon",
# self.simSetupAction.iconSet().pixmap() )
env.history.message(msg)
return
env.history.message(greenmsg("Save Movie File:"))
if self.w.assy.filename: sdir = self.w.assy.filename
else: sdir = env.prefs[workingDirectory_prefs_key]
sfilter = QString("Differential Position Bytes Format (*.dpb)")
# Removed .xyz as an option in the sfilter since the section of code below
# to save XYZ files never worked anyway. This also fixes bug 492. Mark 050816.
fn = QFileDialog.getSaveFileName(
self, "Save As", sdir,
"Differential Position Bytes Format (*.dpb);;POV-Ray Series (*.pov)",
sfilter)
if not fn:
env.history.message("Cancelled.")
return
else:
fn = str(fn)
dir, fil, ext2 = filesplit(fn)
del ext2 #bruce 050413
ext = str(
sfilter[-5:-1]
) # Get "ext" from the sfilter. It *can* be different from "ext2"!!! - Mark
#bruce 050413 comment: the above assumes that len(ext) is always 4 (.xxx).
# I'm speculating that this is ok for now since it has to be one of the ones
# provided to the getSaveFileName method above.
# Changed os.path.join > os.path.normpath to partially fix bug #956. Mark 050911.
safile = os.path.normpath(dir + "/" + fil +
ext) # full path of "Save As" filename
if os.path.exists(
safile): # ...and if the "Save As" file exists...
# ... confirm overwrite of the existing file.
ret = QMessageBox.warning(
self, "Confirm overwrite",
"The file \"" + fil + ext + "\" already exists.\n"\
"Do you want to overwrite the existing file or cancel?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1 ) # Escape == button 1
if ret == 1: # The user cancelled
env.history.message("Cancelled. File not saved.")
return # Cancel clicked or Alt+C pressed or Escape pressed
if ext == '.dpb':
self.w.assy.current_movie._close()
import shutil
shutil.copy(self.w.assy.current_movie.filename, safile)
# Get the trace file name.
tfile1 = self.w.assy.current_movie.get_trace_filename()
# Copy the tracefile
if os.path.exists(tfile1):
fullpath, ext = os.path.splitext(safile)
tfile2 = fullpath + "-trace.txt"
shutil.copy(tfile1, tfile2)
env.history.message("DPB movie file saved: " + safile)
# note that we are still playing it from the old file and filename... does it matter? [bruce 050427 question]
# Added "hflag=False" to suppress history msg, fixing bug #956. Mark 050911.
self.w.assy.current_movie.cueMovie(
propMgr=self,
hflag=False) # Do not print info to history widget.
elif ext == '.pov':
self.w.assy.current_movie._write_povray_series(
os.path.normpath(dir + "/" + fil))
else: #.xyz (or something unexpected)
#bruce 051115 added warning and immediate return, to verify that this code is never called
QMessageBox.warning(
self, "ERROR",
"internal error: unsupported file extension %r" %
(ext, )) # args are title, content
return # from fileSaveMovie
def __init__(self,
title=_('Choose Files'),
filters=[],
add_all_files_filter=True,
parent=None,
modal=True,
name='',
mode=QFileDialog.ExistingFiles,
default_dir='~',
no_save_dir=False,
combine_file_and_saved_dir=False):
QObject.__init__(self)
ftext = ''
if filters:
for filter in filters:
text, extensions = filter
extensions = [
'*' + (i if i.startswith('.') else '.' + i)
for i in extensions
]
ftext += '%s (%s);;' % (text, ' '.join(extensions))
if add_all_files_filter or not ftext:
ftext += 'All files (*)'
if ftext.endswith(';;'):
ftext = ftext[:-2]
self.dialog_name = name if name else 'dialog_' + title
self.selected_files = None
self.fd = None
if combine_file_and_saved_dir:
bn = os.path.basename(default_dir)
prev = dynamic.get(self.dialog_name, os.path.expanduser('~'))
if os.path.exists(prev):
if os.path.isfile(prev):
prev = os.path.dirname(prev)
else:
prev = os.path.expanduser('~')
initial_dir = os.path.join(prev, bn)
elif no_save_dir:
initial_dir = os.path.expanduser(default_dir)
else:
initial_dir = dynamic.get(self.dialog_name,
os.path.expanduser(default_dir))
if not isinstance(initial_dir, basestring):
initial_dir = os.path.expanduser(default_dir)
if not initial_dir or (
not os.path.exists(initial_dir)
and not (mode == QFileDialog.AnyFile and
(no_save_dir or combine_file_and_saved_dir))):
initial_dir = select_initial_dir(initial_dir)
self.selected_files = []
use_native_dialog = 'CALIBRE_NO_NATIVE_FILEDIALOGS' not in os.environ
with SanitizeLibraryPath():
opts = QFileDialog.Option()
if not use_native_dialog:
opts |= QFileDialog.DontUseNativeDialog
if mode == QFileDialog.AnyFile:
f = unicode(
QFileDialog.getSaveFileName(parent, title, initial_dir,
ftext, "", opts))
if f:
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFile:
f = unicode(
QFileDialog.getOpenFileName(parent, title, initial_dir,
ftext, "", opts))
if f and os.path.exists(f):
self.selected_files.append(f)
elif mode == QFileDialog.ExistingFiles:
fs = QFileDialog.getOpenFileNames(parent, title, initial_dir,
ftext, "", opts)
for f in fs:
f = unicode(f)
if not f:
continue
if not os.path.exists(f):
# QFileDialog for some reason quotes spaces
# on linux if there is more than one space in a row
f = unquote(f)
if f and os.path.exists(f):
self.selected_files.append(f)
else:
if mode == QFileDialog.Directory:
opts |= QFileDialog.ShowDirsOnly
f = unicode(
QFileDialog.getExistingDirectory(parent, title,
initial_dir, opts))
if os.path.exists(f):
self.selected_files.append(f)
if self.selected_files:
self.selected_files = [unicode(q) for q in self.selected_files]
saved_loc = self.selected_files[0]
if os.path.isfile(saved_loc):
saved_loc = os.path.dirname(saved_loc)
if not no_save_dir:
dynamic[self.dialog_name] = saved_loc
self.accepted = bool(self.selected_files)
def SaveAction(self):
#Filename zum Speichern vom Benutzer erfragen
filename = QFileDialog.getSaveFileName(self, 'Messung Speichern')
if not filename == '':
self.MainProgramm.SaveFile(filename)
def fileSaveMovie(self):
"""
Save a copy of the current movie file loaded in the Movie Player.
"""
# Make sure there is a moviefile to save.
if not self.w.assy.current_movie or not self.w.assy.current_movie.filename \
or not os.path.exists(self.w.assy.current_movie.filename):
msg = redmsg("Save Movie File: No movie file to save.")
env.history.message(msg)
msg = "To create a movie, click on the <b>Simulator</b> <img source=\"simicon\"> icon."
#QMimeSourceFactory.defaultFactory().setPixmap( "simicon",
# self.simSetupAction.iconSet().pixmap() )
env.history.message(msg)
return
env.history.message(greenmsg("Save Movie File:"))
if self.w.assy.filename: sdir = self.w.assy.filename
else: sdir = env.prefs[workingDirectory_prefs_key]
sfilter = QString("Differential Position Bytes Format (*.dpb)")
# Removed .xyz as an option in the sfilter since the section of code below
# to save XYZ files never worked anyway. This also fixes bug 492. Mark 050816.
fn = QFileDialog.getSaveFileName(
self,
"Save As",
sdir,
"Differential Position Bytes Format (*.dpb);;POV-Ray Series (*.pov)",
sfilter)
if not fn:
env.history.message("Cancelled.")
return
else:
fn = str(fn)
dir, fil, ext2 = filesplit(fn)
del ext2 #bruce 050413
ext = str(sfilter[-5:-1]) # Get "ext" from the sfilter. It *can* be different from "ext2"!!! - Mark
#bruce 050413 comment: the above assumes that len(ext) is always 4 (.xxx).
# I'm speculating that this is ok for now since it has to be one of the ones
# provided to the getSaveFileName method above.
# Changed os.path.join > os.path.normpath to partially fix bug #956. Mark 050911.
safile = os.path.normpath(dir + "/" + fil + ext) # full path of "Save As" filename
if os.path.exists(safile): # ...and if the "Save As" file exists...
# ... confirm overwrite of the existing file.
ret = QMessageBox.warning(
self, "Confirm overwrite",
"The file \"" + fil + ext + "\" already exists.\n"\
"Do you want to overwrite the existing file or cancel?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1 ) # Escape == button 1
if ret == 1: # The user cancelled
env.history.message( "Cancelled. File not saved." )
return # Cancel clicked or Alt+C pressed or Escape pressed
if ext == '.dpb':
self.w.assy.current_movie._close()
import shutil
shutil.copy(self.w.assy.current_movie.filename, safile)
# Get the trace file name.
tfile1 = self.w.assy.current_movie.get_trace_filename()
# Copy the tracefile
if os.path.exists(tfile1):
fullpath, ext = os.path.splitext(safile)
tfile2 = fullpath + "-trace.txt"
shutil.copy(tfile1, tfile2)
env.history.message("DPB movie file saved: " + safile)
# note that we are still playing it from the old file and filename... does it matter? [bruce 050427 question]
# Added "hflag=False" to suppress history msg, fixing bug #956. Mark 050911.
self.w.assy.current_movie.cueMovie(propMgr = self, hflag = False) # Do not print info to history widget.
elif ext == '.pov':
self.w.assy.current_movie._write_povray_series(
os.path.normpath(dir + "/" + fil))
else: #.xyz (or something unexpected)
#bruce 051115 added warning and immediate return, to verify that this code is never called
QMessageBox.warning(self, "ERROR", "internal error: unsupported file extension %r" % (ext,) ) # args are title, content
return # from fileSaveMovie
def writeOut(self):
fileName = QFileDialog.getSaveFileName(self,
"Open Points File",
"",
"Text File (*.txt);;", "")
file = open(fileName, "w")
file.write("________CONTROL POINTS________\n\n")
for i,j in self.control.iteritems():
file.write(i +":\n"+ str(j)+"\n")
file.write("________UNKNOWNS________\n\n")
file.write(str(self.unknowns)+'\n\n')
file.write("_______________________________________ CALCULATIONS _______________________________________ \n\n\n\n")
k=0
for i in range (self.iterations):
k+=1
provis=adjustProvisional(self.Xdict,self.provis, self.obs, self.unknowns)
A,Xdict,provis,obs,control,unknowns,L=Iterate(provis, self.obs, self.control, self.unknowns,self.P)
X=((A.T*self.P*A)**-1)*A.T*self.P*L
Xdict=Points("Solutions Dictionary")
j=0
for i in unknowns:
Xdict[i]=X[j]
j+=1
V,posteriori,covarience_mat,precisi=precisions(A,X,self.P,L,obs,unknowns)
file.write("________ITERATION: "+str(k)+" ________\n\n")
if float(round(float((A.T*self.P*V).T*(A.T*self.P*V)),6))==0.:
file.write("____________________________________________________\n\nCalculation check 'A.tPV' successful\n---------------------------------------------\n")
else:
file.write("Calculation check 'A.tPV' unsuccessful to 6 dec places\n\n")
# V,posteriori,covarience_mat,precisions
file.write("________'V.TPV'________\n\n")
file.write(str(V.T*self.P*V)+'\n\n')
file.write("________Posteriori________\n\n")
file.write(str(posteriori)+'\n\n')
# file.write("________Covarience Matrix________\n\n") # COVARIENCE MATRIX
# file.write(str(covarience_mat)+'\n\n')
file.write("________Precisions of Unknowns ________\n\n")
for i,j in precisi.iteritems():
file.write(i +":\n"+ str(round(float(j),3))+"\n\n")
check=globalCheck(provis,control,V,obs,unknowns,Xdict)
file.write("________Global Check________\n\n")
for i,j in check.iteritems():
file.write(i +":\n"+ str(j)+"\n")
file.write("________________---- END OF ITERATION "+str(k)+" ----____________\n\n")
file.write("_______________________________________________________________________\n\n")
# showGraph(N,provisionals,control)
file.write("________FINAL COORDINATES________\n\n")
for i,j in provis.iteritems():
file.write(i +":\n"+ str(j)+"\n\n")
file.write("________X Solution Vector, With distances in meters and directions in seconds ________\n\n")
for i,j in Xdict.iteritems():
file.write(i +":\n"+ str(round(float(j),3))+"\n\n")
def saveToFileBowditch(self):
''' the bowditch needs to be setup such that the final coordinate is a known point, a single letter, then the reference
will be in the next 2 rows, with a dash next to the single letter'''
fileName = QFileDialog.getSaveFileName(self,
"Open Points File",
"",
"Excel (*.xlsx)", "")
dX,dY=bowditchAdjust(self.provisionals,self.control,self.obsOrder[-1][4:])
self.bowditch.setText("not completed yet.")
sumDistance=0
for i,j in self.obs1.iteritems():
for p,t in j.iteritems():
if self.provisionals.has_key(p):
sumDistance=sumDistance+t.distance
dX=dX/sumDistance
dY=dY/sumDistance
fileName=str(fileName)
workbook = xlsxwriter.Workbook(fileName)
worksheet = workbook.add_worksheet()
i=0
worksheet.write(0,0, 'Leg')
worksheet.write(0,1, 'Dir/OrCorr./Dis')
worksheet.write(0,2, 'Name')
worksheet.write(0,3, 'Y')
worksheet.write(0,4, 'X')
worksheet.write(2,2, self.control[self.stationsOrder[0]].name)
worksheet.write(2,3, self.control[self.stationsOrder[0]].y)
worksheet.write(2,4, self.control[self.stationsOrder[0]].x)
i+=4
temp=self.stationsOrder[0]
soFar=0
format = workbook.add_format()
format.set_underline()
for nm3 in self.stationsOrder:
for nm,ob in self.obs1[nm3].iteritems():
if self.provisionals.has_key(nm):
worksheet.write(i,0, nm3+"-"+nm)
worksheet.write(i,1, rad2dms(self.obs1[nm3][nm].direction))
worksheet.write(i,2, nm)
worksheet.write(i,3, round(self.provisionals[nm].y,3))
worksheet.write(i,4, round(self.provisionals[nm].x,3))
i+=1
ldist=self.obs1[nm3][nm].distance
soFar+=ldist
worksheet.write(i,3,soFar*dY)
worksheet.write(i,4,soFar*dX)
i+=1
worksheet.write(i,1, str(round(self.obs1[nm3][nm].distance,2))+"m")
worksheet.write(i,2, nm,format)
worksheet.write(i,3, round(self.provisionals[nm].y+soFar*dY,2),format)
worksheet.write(i,4, round(self.provisionals[nm].x+soFar*dX,2),format)
i+=2
temp=nm
workbook.close()
