def __init__(self, parent=None, helpDialog=None):
"Initialize LeginonUI widget"
QtGui.QWidget.__init__(self, parent)
# Build window
_logger.info("\rBuilding main window ...")
self.ui = Ui_Form()
self.ui.setupUi(self)
self.login = {}
self.helpDialog = helpDialog
self.startTabIndex = 0
self.ui.progressDialog = QtGui.QProgressDialog('Loading...', "", 0, 5,
self)
self.ui.progressDialog.setWindowModality(QtCore.Qt.ApplicationModal)
self.ui.progressDialog.findChildren(QtGui.QPushButton)[0].hide()
#self.ui.progressDialog.setCancelButton(0) # might work
#self.ui.progressDialog.setWindowFlags(self.ui.progressDialog.windowFlags() & ~QtCore.Qt.WindowCloseButtonHint) #v5s
self.ui.progressDialog.setWindowFlags(QtCore.Qt.Window
| QtCore.Qt.WindowTitleHint
| QtCore.Qt.CustomizeWindowHint)
self.ui.reloadTableToolButton.clicked.connect(
self.queryDatabaseForProjects)
self.taskUpdated.connect(self.updateProgress)
self.ui.leginonHostnameLineEdit.editingFinished.connect(
lambda: self.ui.projectHostnameLineEdit.setText(
self.ui.leginonHostnameLineEdit.text())
if self.ui.projectHostnameLineEdit.text() == "" else None)
header = [('Session', None), ('Project', None), ('Images', None),
('Voltage', 'voltage'), ('Pixel Size', 'apix'),
('Magnification', None), ('CS', 'cs'), ('Image Name', None),
('Image Path', None), ('Frame Path', None)]
self.header = [h[0] for h in header]
self.headermap = dict([h for h in header if h[1] is not None])
self.images = []
self.ui.projectTableView.setModel(
ListTableModel([], self.header, None, self))
selmodel = self.ui.projectTableView.selectionModel()
selmodel.selectionChanged.connect(self.selectionChanged)
_logger.info("\rLoading settings ...")
self.readSettings()
self.on_loginPushButton_clicked()
def __init__(self, parent=None):
"Initialize screener window"
QtGui.QWidget.__init__(self, parent)
self.parent_control = parent
# Build window
_logger.info("Building main window ...")
self.ui = Ui_Form()
self.ui.setupUi(self)
self.header = ['# Mics', '# Particles', 'Disk', 'Mask', 'Overlap']
self.options = [
self.ui.diskDoubleSpinBox.statusTip(),
self.ui.diskDoubleSpinBox.statusTip(),
self.ui.diskDoubleSpinBox.statusTip()
]
self.data = []
self.micrograph_files = []
self.output = None
self.output_base = None
self.ui.autopickHistoryTableView.setModel(
ListTableModel([], self.header, None, self))
#selmodel=self.ui.autopickHistoryTableView.selectionModel()
self.ui.autopickHistoryTableView.doubleClicked.connect(
self.on_runPushButton_clicked)
#doubleClicked ( const QModelIndex & index )
self.ui.progressDialog = QtGui.QProgressDialog('Running...', "Close",
0, 1, self)
self.ui.progressDialog.setWindowModality(QtCore.Qt.ApplicationModal)
#self.ui.progressDialog.findChildren(QtGui.QPushButton)[0].hide()
self.ui.progressDialog.setWindowFlags(QtCore.Qt.Window
| QtCore.Qt.WindowTitleHint
| QtCore.Qt.CustomizeWindowHint)
self.task = None
self.output = None
self.taskUpdated.connect(self.updateProgress)
self.option_control_map = self._collect_options_controls()
self._add_controls()
def saveSelection(self, invert=False, filename=None, prefix=None):
'''
'''
if filename is None: filename = self.selection_file
self.setEnabled(False)
try:
progressDialog = QtGui.QProgressDialog('Saving...', "", 0, 5, self)
progressDialog.setWindowModality(QtCore.Qt.WindowModal)
progressDialog.show()
if isinstance(filename, tuple): filename = filename[0]
if not filename: return
file_index = self.file_index.copy()
if invert:
sel = file_index[:, 2] > -1
file_index[sel, 2] = numpy.logical_not(file_index[sel, 2] > 0)
if filename != "":
if self.advanced_settings.relion != "" and os.path.splitext(
filename)[1] == '.star':
if not (len(self.files) == 1
or len(self.files) == len(file_index)):
progressDialog.hide()
QtGui.QMessageBox.critical(
self, "Saving Relion Selection File",
"You have opened more than one class stack. Cannot save a Relion Selection file!",
QtGui.QMessageBox.Ok | QtGui.QMessageBox.Default
| QtGui.QMessageBox.NoButton)
self.setEnabled(True)
return
progressDialog.setValue(1)
_logger.info("Saving Relion selection file to %s" %
filename)
class_column_name = 'rlnClassNumber'
vals = format.read(self.advanced_settings.relion,
numeric=True)
progressDialog.setValue(2)
subset = []
selected = set([v[1] + 1 for v in file_index if v[2] > 0])
progressDialog.setValue(3)
for v in vals:
id = int(getattr(v, class_column_name))
if id in selected: subset.append(v)
progressDialog.setValue(4)
format.write(filename, subset, prefix=prefix)
progressDialog.setValue(5)
#relion_selection.select_class_subset(vals, select, filename)
elif len(self.files) == 1 or len(
self.files) == len(file_index):
progressDialog.setValue(3)
_logger.info("Saving single selection file to %s" %
filename)
if not spider_utility.is_spider_filename(
self.files) and len(self.files) > 1:
_logger.info(
"File names do not conform to SPIDER, writing as star file"
)
filename = os.path.splitext(filename)[0] + '.star'
vals = [(self.files[v[0]], 1) for v in file_index
if v[2] > 0]
elif len(self.files) > 1:
vals = [(spider_utility.spider_id(self.files[v[0]]), 1)
for v in file_index if v[2] > 0]
else:
vals = [(v[1] + 1, 1) for v in file_index if v[2] > 0]
progressDialog.setValue(4)
format.write(filename,
vals,
header='id,select'.split(','),
default_format=format.spidersel,
prefix=prefix)
progressDialog.setValue(5)
else:
progressDialog.setValue(3)
_logger.info(
"Saving multiple selection files by stack to %s" %
filename)
if not spider_utility.is_spider_filename(self.files):
_logger.info(
"File names do not conform to SPIDER, writing as star file"
)
filename = os.path.splitext(filename)[0] + '.star'
vals = [(relion_utility.relion_identifier(
self.files[v[0]], v[1] + 1), 1) for v in file_index
if v[2] > 0]
format.write(filename,
vals,
header='id,select'.split(','))
else:
micselect = {}
for v in file_index:
if v[2] > 0:
mic = spider_utility.spider_id(
self.files[v[0]])
if mic not in micselect: micselect[mic] = []
micselect[mic].append((v[1] + 1, 1))
for mic, vals in micselect.iteritems():
format.write(filename,
numpy.asarray(vals),
spiderid=mic,
header="id,select".split(','),
default_format=format.spidersel,
prefix=prefix)
progressDialog.setValue(5)
finally:
self.setEnabled(True)
#progressDialog.hide()
print 'done'
def on_loadImagesPushButton_clicked(self):
''' Load the current batch of images into the list
'''
if len(self.files) == 0: return
self.imageListModel.clear()
index, start = self.imageSubset(self.ui.pageSpinBox.value() - 1,
self.ui.imageCountSpinBox.value())
if len(index) == 0:
self.ui.pageSpinBox.blockSignals(True)
self.ui.pageSpinBox.setValue(0)
self.ui.pageSpinBox.blockSignals(False)
self.ui.imageCountSpinBox.blockSignals(True)
self.ui.imageCountSpinBox.setValue(1)
self.ui.imageCountSpinBox.blockSignals(False)
index, start = self.imageSubset(0, 1)
bin_factor = self.ui.decimateSpinBox.value()
nstd = self.ui.clampDoubleSpinBox.value()
img = None
self.loaded_images = []
self.base_level = None
zoom = self.ui.imageZoomDoubleSpinBox.value()
masks = {}
template = self.get_template()
progressDialog = QtGui.QProgressDialog('Opening...', "Cancel", 0,
len(index), self)
progressDialog.setWindowModality(QtCore.Qt.WindowModal)
progressDialog.show()
self.ui.imageListView.setModel(None)
if not drawing.is_available():
_logger.info("No PIL loaded")
self.advanced_settings.mark_image = False
if not plotting.is_available():
_logger.info("No matplotlib loaded")
self.advanced_settings.mark_image = False
current_powerspec = self.advanced_settings.current_powerspec
if current_powerspec:
if self.advanced_settings.invert:
_logger.info("Cannot invert a power spectra")
else:
if self.advanced_settings.center_mask > 0:
_logger.info("Cannot mask micrograph")
added_items = []
for i, (imgname, img, pixel_size) in enumerate(
iter_images(self.files, index, template)):
selimg = None
progressDialog.setValue(i + 1)
if hasattr(img, 'ndim'):
if current_powerspec and self.advanced_settings.center_mask > 0 and img.shape not in masks:
masks[img.shape] = ndimage_utility.model_disk(
self.advanced_settings.center_mask, img.shape) * -1 + 1
if self.advanced_settings.invert and not current_powerspec:
if img.max() != img.min(): ndimage_utility.invert(img, img)
img = ndimage_utility.replace_outlier(img,
nstd,
nstd,
replace='mean')
if self.advanced_settings.gaussian_high_pass > 0.0:
img = ndimage_filter.filter_gaussian_highpass(
img,
pixel_size / self.advanced_settings.gaussian_high_pass)
if self.advanced_settings.gaussian_low_pass > 0.0:
img = ndimage_filter.filter_gaussian_lowpass(
img,
pixel_size / self.advanced_settings.gaussian_low_pass)
if current_powerspec and self.advanced_settings.center_mask > 0:
#img[numpy.logical_not(masks[img.shape])] = numpy.mean(img[masks[img.shape]])
img *= masks[img.shape]
if bin_factor > 1.0:
img = ndimage_interpolate.interpolate(
img, bin_factor,
self.advanced_settings.downsample_type)
pixel_size *= bin_factor
img = self.display_powerspectra_1D(img, imgname, pixel_size)
img = self.display_resolution(img, imgname, pixel_size)
img = self.box_particles(img, imgname)
if self.advanced_settings.mark_image:
imgm = self.imageMarker(img)
selimg = qimage_utility.numpy_to_qimage(imgm)
qimg = qimage_utility.numpy_to_qimage(img)
if img.ndim == 2:
if self.base_level is not None:
qimg.setColorTable(self.color_level)
else:
self.base_level = qimg.colorTable()
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level,
self.ui.contrastSlider.value())
qimg.setColorTable(self.color_level)
else:
if self.base_level is None: self.base_level = []
self.base_level.append(qimg.colorTable())
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level[-1],
self.ui.contrastSlider.value())
qimg.setColorTable(self.color_level)
else:
qimg = img.convertToFormat(QtGui.QImage.Format_Indexed8)
if self.base_level is None: self.base_level = []
self.base_level.append(qimg.colorTable())
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level[-1],
self.ui.contrastSlider.value())
qimg.setColorTable(self.color_level)
self.loaded_images.append(qimg)
pix = QtGui.QPixmap.fromImage(qimg)
icon = QtGui.QIcon()
icon.addPixmap(pix, QtGui.QIcon.Normal)
if selimg is not None:
pix = QtGui.QPixmap.fromImage(selimg)
icon.addPixmap(pix, QtGui.QIcon.Selected)
if self.advanced_settings.show_label:
item = QtGui.QStandardItem(
icon,
"%s/%d" % (os.path.basename(imgname[0]), imgname[1] + 1))
else:
item = QtGui.QStandardItem(icon, "")
if hasattr(start, '__iter__'):
item.setData(start[i], QtCore.Qt.UserRole)
else:
item.setData(i + start, QtCore.Qt.UserRole)
self.addToolTipImage(imgname, item, pixel_size)
self.imageListModel.appendRow(item)
added_items.append(item)
self.ui.imageListView.setModel(self.imageListModel)
progressDialog.hide()
for item in added_items:
self.notify_added_item(item)
self.imagesize = img.shape[0] if hasattr(img, 'shape') else img.width()
n = max(5, int(self.imagesize * zoom))
self.ui.imageListView.setIconSize(QtCore.QSize(n, n))
batch_count = numpy.ceil(
float(self.imageTotal()) / self.ui.imageCountSpinBox.value())
self.ui.pageSpinBox.setSuffix(" of %d" % batch_count)
self.ui.pageSpinBox.setMaximum(batch_count)
self.ui.actionForward.setEnabled(
self.ui.pageSpinBox.value() < batch_count)
self.ui.actionBackward.setEnabled(self.ui.pageSpinBox.value() > 0)
