def init_gui(self):
vbox = QtWidgets.QVBoxLayout()
hbox = QtWidgets.QHBoxLayout()
inner_layout = QtWidgets.QVBoxLayout()
button_hbox = QtWidgets.QHBoxLayout()
res_hbox = QtWidgets.QHBoxLayout()
self.res_slider = QtWidgets.QSlider(QtCore.Qt.Horizontal, self)
self.res_slider.setMinimum(0)
self.res_slider.setMaximum(
(self.RES_MAX - self.RES_MIN) / self.RES_INTERVAL)
# self.res_slider.setTickInterval(1)
# self.res_slider.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.res_slider.valueChanged[int].connect(self.slider_changing)
self.res_slider.sliderReleased.connect(self.slider_released)
self.lineedit = QtWidgets.QLineEdit(self)
self.lineedit.setFocusPolicy(QtCore.Qt.StrongFocus)
self.lineedit.setMinimumSize(30, 1)
self.lineedit.setMaximumSize(40, 40)
self.lineedit.returnPressed.connect(self.lineedit_return)
res_hbox.addWidget(QtWidgets.QLabel('resolution:', self))
res_hbox.addWidget(self.res_slider)
res_hbox.addWidget(self.lineedit)
# set font
# font = QFont("Courier New", 14)
# table_view.setFont(font)
# set column width to fit contents (set font first!)
# enable sortingq
# table_view.setSortingEnabled(True)
ok_button = QtWidgets.QPushButton('Ok', self)
ok_button.setAutoDefault(False)
ok_button.clicked.connect(self.ok)
cancel_button = QtWidgets.QPushButton('Cancel', self)
cancel_button.setAutoDefault(False)
cancel_button.clicked.connect(self.cancel)
button_hbox.addStretch()
button_hbox.addWidget(ok_button)
button_hbox.addStretch()
button_hbox.addWidget(cancel_button)
button_hbox.addStretch()
self.table_view = CalculationTable(self)
self.res_slider.setValue(
(self.resolution - self.RES_MIN) / self.RES_INTERVAL)
self.update_table()
self.surf_check = QtWidgets.QCheckBox(
'calculate surface based cavities', self)
self.surf_check.setChecked(True)
self.center_check = QtWidgets.QCheckBox(
'calculate center based cavities', self)
self.gyration_tensor_check = QtWidgets.QCheckBox(
'calculate gyration tensor parameters', self)
self.gyration_tensor_check.setToolTip(
'squared_gyration_radius, asphericity, acylindricity, anisotropy')
self.overwrite_check = QtWidgets.QCheckBox(
'overwrite existing results', self)
self.exporthdf5_check = QtWidgets.QCheckBox(
'export results as HDF5 files', self)
self.exporttext_check = QtWidgets.QCheckBox(
'export results as text files', self)
self.exportdir_radio_input = QtWidgets.QRadioButton(
'export to the directory of the input files', self)
self.exportdir_radio_config = QtWidgets.QRadioButton(
'export to %s' % config.Path.result_dir, self)
self.exportdir_radio_input.setChecked(True)
covalence_radii_by_element = self.__get_all_covalence_radii_by_element(
)
self.radii_widget = RadiiWidget(covalence_radii_by_element,
self.file_frame_dict, self)
inner_layout.addLayout(res_hbox)
inner_layout.addWidget(self.table_view)
inner_layout.addWidget(self.surf_check)
inner_layout.addWidget(self.center_check)
inner_layout.addWidget(self.gyration_tensor_check)
inner_layout.addWidget(self.overwrite_check)
inner_layout.addWidget(self.exporthdf5_check)
inner_layout.addWidget(self.exporttext_check)
inner_layout.addWidget(self.exportdir_radio_input)
inner_layout.addWidget(self.exportdir_radio_config)
hbox.addLayout(inner_layout)
hbox.addWidget(self.radii_widget)
vbox.addLayout(hbox)
vbox.addLayout(button_hbox)
self.setLayout(vbox)
def init_gui(self):
vbox = QtWidgets.QVBoxLayout()
hbox = QtWidgets.QHBoxLayout()
inner_layout = QtWidgets.QVBoxLayout()
button_hbox = QtWidgets.QHBoxLayout()
res_hbox = QtWidgets.QHBoxLayout()
self.res_slider = QtWidgets.QSlider(QtCore.Qt.Horizontal, self)
self.res_slider.setMinimum(0)
self.res_slider.setMaximum((self.RES_MAX - self.RES_MIN) / self.RES_INTERVAL)
# self.res_slider.setTickInterval(1)
# self.res_slider.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.res_slider.valueChanged[int].connect(self.slider_changing)
self.res_slider.sliderReleased.connect(self.slider_released)
self.lineedit = QtWidgets.QLineEdit(self)
self.lineedit.setFocusPolicy(QtCore.Qt.StrongFocus)
self.lineedit.setMinimumSize(30, 1)
self.lineedit.setMaximumSize(40, 40)
self.lineedit.returnPressed.connect(self.lineedit_return)
res_hbox.addWidget(QtWidgets.QLabel('resolution:', self))
res_hbox.addWidget(self.res_slider)
res_hbox.addWidget(self.lineedit)
# set font
# font = QFont("Courier New", 14)
# table_view.setFont(font)
# set column width to fit contents (set font first!)
# enable sortingq
# table_view.setSortingEnabled(True)
ok_button = QtWidgets.QPushButton('Ok', self)
ok_button.setAutoDefault(False)
ok_button.clicked.connect(self.ok)
cancel_button = QtWidgets.QPushButton('Cancel', self)
cancel_button.setAutoDefault(False)
cancel_button.clicked.connect(self.cancel)
button_hbox.addStretch()
button_hbox.addWidget(ok_button)
button_hbox.addStretch()
button_hbox.addWidget(cancel_button)
button_hbox.addStretch()
self.table_view = CalculationTable(self)
self.res_slider.setValue((self.resolution-self.RES_MIN)/self.RES_INTERVAL)
self.update_table()
self.surf_check = QtWidgets.QCheckBox('calculate surface based cavities', self)
self.surf_check.setChecked(True)
self.center_check = QtWidgets.QCheckBox('calculate center based cavities', self)
self.gyration_tensor_check = QtWidgets.QCheckBox('calculate gyration tensor parameters', self)
self.gyration_tensor_check.setToolTip('squared_gyration_radius, asphericity, acylindricity, anisotropy')
self.overwrite_check = QtWidgets.QCheckBox('overwrite existing results', self)
self.exporthdf5_check = QtWidgets.QCheckBox('export results as HDF5 files', self)
self.exporttext_check = QtWidgets.QCheckBox('export results as text files', self)
self.exportdir_radio_input = QtWidgets.QRadioButton('export to the directory of the input files', self)
self.exportdir_radio_config = QtWidgets.QRadioButton('export to %s' % config.Path.result_dir, self)
self.exportdir_radio_input.setChecked(True)
covalence_radii_by_element = self.__get_all_covalence_radii_by_element()
self.radii_widget = RadiiWidget(covalence_radii_by_element, self.file_frame_dict, self)
inner_layout.addLayout(res_hbox)
inner_layout.addWidget(self.table_view)
inner_layout.addWidget(self.surf_check)
inner_layout.addWidget(self.center_check)
inner_layout.addWidget(self.gyration_tensor_check)
inner_layout.addWidget(self.overwrite_check)
inner_layout.addWidget(self.exporthdf5_check)
inner_layout.addWidget(self.exporttext_check)
inner_layout.addWidget(self.exportdir_radio_input)
inner_layout.addWidget(self.exportdir_radio_config)
hbox.addLayout(inner_layout)
hbox.addWidget(self.radii_widget)
vbox.addLayout(hbox)
vbox.addLayout(button_hbox)
self.setLayout(vbox)
class CalculationSettingsDialog(QtWidgets.QDialog):
RES_MIN = 32
RES_MAX = 1024
RES_INTERVAL = 32
def __init__(self, parent, file_frame_dict):
QtWidgets.QDialog.__init__(self, parent)
self.control = parent.control
self.resolution = config.Computation.std_resolution
self.filenames = file_frame_dict.keys()
self.file_frame_dict = file_frame_dict
self.init_gui()
self.setWindowTitle("Calculation Settings")
def init_gui(self):
vbox = QtWidgets.QVBoxLayout()
hbox = QtWidgets.QHBoxLayout()
inner_layout = QtWidgets.QVBoxLayout()
button_hbox = QtWidgets.QHBoxLayout()
res_hbox = QtWidgets.QHBoxLayout()
self.res_slider = QtWidgets.QSlider(QtCore.Qt.Horizontal, self)
self.res_slider.setMinimum(0)
self.res_slider.setMaximum(
(self.RES_MAX - self.RES_MIN) / self.RES_INTERVAL)
# self.res_slider.setTickInterval(1)
# self.res_slider.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.res_slider.valueChanged[int].connect(self.slider_changing)
self.res_slider.sliderReleased.connect(self.slider_released)
self.lineedit = QtWidgets.QLineEdit(self)
self.lineedit.setFocusPolicy(QtCore.Qt.StrongFocus)
self.lineedit.setMinimumSize(30, 1)
self.lineedit.setMaximumSize(40, 40)
self.lineedit.returnPressed.connect(self.lineedit_return)
res_hbox.addWidget(QtWidgets.QLabel('resolution:', self))
res_hbox.addWidget(self.res_slider)
res_hbox.addWidget(self.lineedit)
# set font
# font = QFont("Courier New", 14)
# table_view.setFont(font)
# set column width to fit contents (set font first!)
# enable sortingq
# table_view.setSortingEnabled(True)
ok_button = QtWidgets.QPushButton('Ok', self)
ok_button.setAutoDefault(False)
ok_button.clicked.connect(self.ok)
cancel_button = QtWidgets.QPushButton('Cancel', self)
cancel_button.setAutoDefault(False)
cancel_button.clicked.connect(self.cancel)
button_hbox.addStretch()
button_hbox.addWidget(ok_button)
button_hbox.addStretch()
button_hbox.addWidget(cancel_button)
button_hbox.addStretch()
self.table_view = CalculationTable(self)
self.res_slider.setValue(
(self.resolution - self.RES_MIN) / self.RES_INTERVAL)
self.update_table()
self.surf_check = QtWidgets.QCheckBox(
'calculate surface based cavities', self)
self.surf_check.setChecked(True)
self.center_check = QtWidgets.QCheckBox(
'calculate center based cavities', self)
self.gyration_tensor_check = QtWidgets.QCheckBox(
'calculate gyration tensor parameters', self)
self.gyration_tensor_check.setToolTip(
'squared_gyration_radius, asphericity, acylindricity, anisotropy')
self.overwrite_check = QtWidgets.QCheckBox(
'overwrite existing results', self)
self.exporthdf5_check = QtWidgets.QCheckBox(
'export results as HDF5 files', self)
self.exporttext_check = QtWidgets.QCheckBox(
'export results as text files', self)
self.exportdir_radio_input = QtWidgets.QRadioButton(
'export to the directory of the input files', self)
self.exportdir_radio_config = QtWidgets.QRadioButton(
'export to %s' % config.Path.result_dir, self)
self.exportdir_radio_input.setChecked(True)
covalence_radii_by_element = self.__get_all_covalence_radii_by_element(
)
self.radii_widget = RadiiWidget(covalence_radii_by_element,
self.file_frame_dict, self)
inner_layout.addLayout(res_hbox)
inner_layout.addWidget(self.table_view)
inner_layout.addWidget(self.surf_check)
inner_layout.addWidget(self.center_check)
inner_layout.addWidget(self.gyration_tensor_check)
inner_layout.addWidget(self.overwrite_check)
inner_layout.addWidget(self.exporthdf5_check)
inner_layout.addWidget(self.exporttext_check)
inner_layout.addWidget(self.exportdir_radio_input)
inner_layout.addWidget(self.exportdir_radio_config)
hbox.addLayout(inner_layout)
hbox.addWidget(self.radii_widget)
vbox.addLayout(hbox)
vbox.addLayout(button_hbox)
self.setLayout(vbox)
def __get_all_covalence_radii_by_element(self):
covalence_radii_by_element, elements_by_frame, element_combinations = self.__read_atom_info(
)
return covalence_radii_by_element
def __get_elements_by_frame(self):
covalence_radii_by_element, elements_by_frame, element_combinations = self.__read_atom_info(
)
return elements_by_frame
def __get_element_combinations(self):
covalence_radii_by_element, elements_by_frame, element_combinations = self.__read_atom_info(
)
return element_combinations
def __read_atom_info(self):
method = self.__read_atom_info.__func__
for attr in ('covalence_radii_by_element', 'elements_by_frame',
'element_combinations'):
if not hasattr(method, attr):
setattr(method, attr, None)
if (method.covalence_radii_by_element is None
or method.elements_by_frame is None
or method.element_combinations is None):
radii = {}
elements_by_frame = {}
element_combinations = set()
for filepath, frames in self.file_frame_dict.iteritems():
elements_by_frame[filepath] = {}
inputfile = file.File.open(filepath)
if frames == (-1, ):
frames = range(inputfile.info.num_frames)
for frame in frames:
atoms = inputfile.getatoms(frame)
current_radii = atoms.covalence_radii_by_element
current_elements = atoms.elements
radii.update(current_radii)
elements_by_frame[filepath][frame] = current_elements
element_combinations.add(tuple(current_elements))
method.covalence_radii_by_element = radii
method.elements_by_frame = elements_by_frame
return (method.covalence_radii_by_element, method.elements_by_frame,
method.element_combinations)
def __update_cutoff_history(self):
timestamp = datetime.datetime.now()
user_cutoff_radii = self.radii_widget.cutoff_radii
elements = self.__get_all_covalence_radii_by_element().keys()
if not isinstance(user_cutoff_radii, collections.Iterable):
user_cutoff_radii = dict(
(elem, user_cutoff_radii) for elem in elements)
elements_by_frame = self.__get_elements_by_frame()
new_history = []
for filepath, frames in self.file_frame_dict.iteritems():
filename = os.path.basename(filepath)
file_elements = elements_by_frame[filepath]
for frame in frames:
elements = file_elements[frame]
frame_cutoff_radii = dict(
(elem, user_cutoff_radii[elem]) for elem in elements)
history_entry = HistoryEntry(filename, frame, timestamp,
frame_cutoff_radii)
new_history.append(history_entry)
cutoff_history.extend(new_history)
cutoff_history.save()
def __update_cutoff_presets(self):
save_preset_name = self.radii_widget.save_preset_name
if save_preset_name is not None:
user_cutoff_radii = self.radii_widget.cutoff_radii
cutoff_presets.add(Preset(save_preset_name, user_cutoff_radii))
cutoff_presets.save()
def update_table(self):
# get timestamps for selected frames for each file
# surface based
surface_ts = []
center_ts = []
for i, ts in enumerate(self.timestamps(center_based=False)):
frames = (range(file.File.open(self.filenames[i]).info.num_frames)
if self.file_frame_dict[self.filenames[i]][0] == -1 else
self.file_frame_dict[self.filenames[i]])
surface_ts.append([])
for frame in frames:
surface_ts[i].append(ts[frame])
# center based timestamps for the given frames
center_ts = []
for i, ts in enumerate(self.timestamps(center_based=True)):
frames = (range(file.File.open(self.filenames[i]).info.num_frames) \
if self.file_frame_dict[self.filenames[i]][0] == -1 \
else self.file_frame_dict[self.filenames[i]])
center_ts.append([])
for frame in frames:
center_ts[i].append(ts[frame])
# reduce to a single value per file
surface_ts = ["X" if "X" in ts else ts[0] for ts in surface_ts]
center_ts = ["X" if "X" in ts else ts[0] for ts in center_ts]
basenames = [os.path.basename(path) for path in self.filenames]
frames = [
str([frame + 1 for frame in self.file_frame_dict[f]])[1:-1]
if not self.file_frame_dict[f][0] == -1 else 'all'
for f in self.filenames
]
data_list = zip(basenames, surface_ts, center_ts, frames)
# set table data
header = ['dataset', 'surface based', 'center based', 'frames']
table_model = TableModel(self, data_list, header)
self.table_view.setModel(table_model)
self.table_view.resizeColumnsToContents()
# calculate table size to set its minimum size
width = (self.table_view.model().columnCount(self.table_view) -
1) + self.table_view.verticalHeader().width()
for i in range(self.table_view.model().columnCount(self.table_view)):
width += self.table_view.columnWidth(i)
self.table_view.setMinimumWidth(width)
height = (self.table_view.model().rowCount(self.table_view) -
1) + self.table_view.horizontalHeader().height()
for i in range(self.table_view.model().rowCount(self.table_view)):
height += self.table_view.rowHeight(i)
self.table_view.setMinimumHeight(height)
def lineedit_return(self):
try:
self.resolution = int(self.lineedit.text())
value = (self.resolution - self.RES_MIN) / self.RES_INTERVAL
self.res_slider.setValue(value)
self.update_table()
except ValueError:
pass
def slider_changing(self, value):
self.lineedit.setText(str(value * self.RES_INTERVAL + self.RES_MIN))
def slider_released(self):
self.resolution = self.res_slider.value(
) * self.RES_INTERVAL + self.RES_MIN
self.update_table()
def timestamps(self, center_based=False):
return [
self.control.calculation.calculatedframes(
file.get_abspath(fn), self.resolution, not center_based,
center_based).prettystrings() for fn in self.filenames
]
def ok(self):
self.lineedit_return()
self.__update_cutoff_history()
self.__update_cutoff_presets()
self.done(QtWidgets.QDialog.Accepted)
def cancel(self):
self.done(QtWidgets.QDialog.Rejected)
def calculation_settings(self):
calc_settings = None
while True:
ok = self.exec_()
if ok != QtWidgets.QDialog.Accepted:
break
try:
cutoff_radii = self.radii_widget.cutoff_radii
surface_based = self.surf_check.isChecked()
center_based = self.center_check.isChecked()
gyration_tensor = self.gyration_tensor_check.isChecked()
overwrite = self.overwrite_check.isChecked()
exporthdf5 = self.exporthdf5_check.isChecked()
exporttext = self.exporttext_check.isChecked()
if self.exportdir_radio_config.isChecked():
exportdir = os.path.expanduser(config.Path.result_dir)
else:
exportdir = None
calc_settings = calculation.CalculationSettings(
datasets=self.file_frame_dict,
resolution=self.resolution,
cutoff_radii=cutoff_radii,
domains=True,
surface_cavities=surface_based,
center_cavities=center_based,
gyration_tensor=gyration_tensor,
recalculate=overwrite,
exporthdf5=exporthdf5,
exporttext=exporttext,
exportdir=exportdir)
break
except ValueError:
pass
return (calc_settings, ok)
class CalculationSettingsDialog(QtWidgets.QDialog):
RES_MIN = 32
RES_MAX = 1024
RES_INTERVAL = 32
def __init__(self, parent, file_frame_dict):
QtWidgets.QDialog.__init__(self, parent)
self.control = parent.control
self.resolution = config.Computation.std_resolution
self.filenames = file_frame_dict.keys()
self.file_frame_dict = file_frame_dict
self.init_gui()
self.setWindowTitle("Calculation Settings")
def init_gui(self):
vbox = QtWidgets.QVBoxLayout()
hbox = QtWidgets.QHBoxLayout()
inner_layout = QtWidgets.QVBoxLayout()
button_hbox = QtWidgets.QHBoxLayout()
res_hbox = QtWidgets.QHBoxLayout()
self.res_slider = QtWidgets.QSlider(QtCore.Qt.Horizontal, self)
self.res_slider.setMinimum(0)
self.res_slider.setMaximum((self.RES_MAX - self.RES_MIN) / self.RES_INTERVAL)
# self.res_slider.setTickInterval(1)
# self.res_slider.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.res_slider.valueChanged[int].connect(self.slider_changing)
self.res_slider.sliderReleased.connect(self.slider_released)
self.lineedit = QtWidgets.QLineEdit(self)
self.lineedit.setFocusPolicy(QtCore.Qt.StrongFocus)
self.lineedit.setMinimumSize(30, 1)
self.lineedit.setMaximumSize(40, 40)
self.lineedit.returnPressed.connect(self.lineedit_return)
res_hbox.addWidget(QtWidgets.QLabel('resolution:', self))
res_hbox.addWidget(self.res_slider)
res_hbox.addWidget(self.lineedit)
# set font
# font = QFont("Courier New", 14)
# table_view.setFont(font)
# set column width to fit contents (set font first!)
# enable sortingq
# table_view.setSortingEnabled(True)
ok_button = QtWidgets.QPushButton('Ok', self)
ok_button.setAutoDefault(False)
ok_button.clicked.connect(self.ok)
cancel_button = QtWidgets.QPushButton('Cancel', self)
cancel_button.setAutoDefault(False)
cancel_button.clicked.connect(self.cancel)
button_hbox.addStretch()
button_hbox.addWidget(ok_button)
button_hbox.addStretch()
button_hbox.addWidget(cancel_button)
button_hbox.addStretch()
self.table_view = CalculationTable(self)
self.res_slider.setValue((self.resolution-self.RES_MIN)/self.RES_INTERVAL)
self.update_table()
self.surf_check = QtWidgets.QCheckBox('calculate surface based cavities', self)
self.surf_check.setChecked(True)
self.center_check = QtWidgets.QCheckBox('calculate center based cavities', self)
self.gyration_tensor_check = QtWidgets.QCheckBox('calculate gyration tensor parameters', self)
self.gyration_tensor_check.setToolTip('squared_gyration_radius, asphericity, acylindricity, anisotropy')
self.overwrite_check = QtWidgets.QCheckBox('overwrite existing results', self)
self.exporthdf5_check = QtWidgets.QCheckBox('export results as HDF5 files', self)
self.exporttext_check = QtWidgets.QCheckBox('export results as text files', self)
self.exportdir_radio_input = QtWidgets.QRadioButton('export to the directory of the input files', self)
self.exportdir_radio_config = QtWidgets.QRadioButton('export to %s' % config.Path.result_dir, self)
self.exportdir_radio_input.setChecked(True)
covalence_radii_by_element = self.__get_all_covalence_radii_by_element()
self.radii_widget = RadiiWidget(covalence_radii_by_element, self.file_frame_dict, self)
inner_layout.addLayout(res_hbox)
inner_layout.addWidget(self.table_view)
inner_layout.addWidget(self.surf_check)
inner_layout.addWidget(self.center_check)
inner_layout.addWidget(self.gyration_tensor_check)
inner_layout.addWidget(self.overwrite_check)
inner_layout.addWidget(self.exporthdf5_check)
inner_layout.addWidget(self.exporttext_check)
inner_layout.addWidget(self.exportdir_radio_input)
inner_layout.addWidget(self.exportdir_radio_config)
hbox.addLayout(inner_layout)
hbox.addWidget(self.radii_widget)
vbox.addLayout(hbox)
vbox.addLayout(button_hbox)
self.setLayout(vbox)
def __get_all_covalence_radii_by_element(self):
covalence_radii_by_element, elements_by_frame, element_combinations = self.__read_atom_info()
return covalence_radii_by_element
def __get_elements_by_frame(self):
covalence_radii_by_element, elements_by_frame, element_combinations = self.__read_atom_info()
return elements_by_frame
def __get_element_combinations(self):
covalence_radii_by_element, elements_by_frame, element_combinations = self.__read_atom_info()
return element_combinations
def __read_atom_info(self):
method = self.__read_atom_info.__func__
for attr in ('covalence_radii_by_element', 'elements_by_frame', 'element_combinations'):
if not hasattr(method, attr):
setattr(method, attr, None)
if (method.covalence_radii_by_element is None or
method.elements_by_frame is None or
method.element_combinations is None):
radii = {}
elements_by_frame = {}
element_combinations = set()
for filepath, frames in self.file_frame_dict.iteritems():
elements_by_frame[filepath] = {}
inputfile = file.File.open(filepath)
if frames == (-1, ):
frames = range(inputfile.info.num_frames)
for frame in frames:
atoms = inputfile.getatoms(frame)
current_radii = atoms.covalence_radii_by_element
current_elements = atoms.elements
radii.update(current_radii)
elements_by_frame[filepath][frame] = current_elements
element_combinations.add(tuple(current_elements))
method.covalence_radii_by_element = radii
method.elements_by_frame = elements_by_frame
return (method.covalence_radii_by_element, method.elements_by_frame, method.element_combinations)
def __update_cutoff_history(self):
timestamp = datetime.datetime.now()
user_cutoff_radii = self.radii_widget.cutoff_radii
elements = self.__get_all_covalence_radii_by_element().keys()
if not isinstance(user_cutoff_radii, collections.Iterable):
user_cutoff_radii = dict((elem, user_cutoff_radii) for elem in elements)
elements_by_frame = self.__get_elements_by_frame()
new_history = []
for filepath, frames in self.file_frame_dict.iteritems():
filename = os.path.basename(filepath)
file_elements = elements_by_frame[filepath]
for frame in frames:
elements = file_elements[frame]
frame_cutoff_radii = dict((elem, user_cutoff_radii[elem]) for elem in elements)
history_entry = HistoryEntry(filename, frame, timestamp, frame_cutoff_radii)
new_history.append(history_entry)
cutoff_history.extend(new_history)
cutoff_history.save()
def __update_cutoff_presets(self):
save_preset_name = self.radii_widget.save_preset_name
if save_preset_name is not None:
user_cutoff_radii = self.radii_widget.cutoff_radii
cutoff_presets.add(Preset(save_preset_name, user_cutoff_radii))
cutoff_presets.save()
def update_table(self):
# get timestamps for selected frames for each file
# surface based
surface_ts = []
center_ts = []
for i, ts in enumerate(self.timestamps(center_based=False)):
frames = (range(file.File.open(self.filenames[i]).info.num_frames)
if self.file_frame_dict[self.filenames[i]][0] == -1
else self.file_frame_dict[self.filenames[i]])
surface_ts.append([])
for frame in frames:
surface_ts[i].append(ts[frame])
# center based timestamps for the given frames
center_ts = []
for i, ts in enumerate(self.timestamps(center_based=True)):
frames = (range(file.File.open(self.filenames[i]).info.num_frames) \
if self.file_frame_dict[self.filenames[i]][0] == -1 \
else self.file_frame_dict[self.filenames[i]])
center_ts.append([])
for frame in frames:
center_ts[i].append(ts[frame])
# reduce to a single value per file
surface_ts = ["X" if "X" in ts else ts[0] for ts in surface_ts]
center_ts = ["X" if "X" in ts else ts[0] for ts in center_ts]
basenames = [os.path.basename(path) for path in self.filenames]
frames = [str([frame + 1 for frame in self.file_frame_dict[f]])[1:-1] if not self.file_frame_dict[f][0] == -1 else 'all' for f in self.filenames]
data_list = zip(basenames, surface_ts, center_ts, frames)
# set table data
header = ['dataset', 'surface based', 'center based', 'frames']
table_model = TableModel(self, data_list, header)
self.table_view.setModel(table_model)
self.table_view.resizeColumnsToContents()
# calculate table size to set its minimum size
width = (self.table_view.model().columnCount(self.table_view) - 1) + self.table_view.verticalHeader().width()
for i in range(self.table_view.model().columnCount(self.table_view)):
width += self.table_view.columnWidth(i)
self.table_view.setMinimumWidth(width)
height = (self.table_view.model().rowCount(self.table_view) - 1) + self.table_view.horizontalHeader().height()
for i in range(self.table_view.model().rowCount(self.table_view)):
height += self.table_view.rowHeight(i)
self.table_view.setMinimumHeight(height)
def lineedit_return(self):
try:
self.resolution = int(self.lineedit.text())
value = (self.resolution - self.RES_MIN) / self.RES_INTERVAL
self.res_slider.setValue(value)
self.update_table()
except ValueError:
pass
def slider_changing(self, value):
self.lineedit.setText(str(value * self.RES_INTERVAL + self.RES_MIN))
def slider_released(self):
self.resolution = self.res_slider.value() * self.RES_INTERVAL + self.RES_MIN
self.update_table()
def timestamps(self, center_based=False):
return [self.control.calculation.calculatedframes(
file.get_abspath(fn),
self.resolution,
not center_based,
center_based).prettystrings()
for fn in self.filenames]
def ok(self):
self.lineedit_return()
self.__update_cutoff_history()
self.__update_cutoff_presets()
self.done(QtWidgets.QDialog.Accepted)
def cancel(self):
self.done(QtWidgets.QDialog.Rejected)
def calculation_settings(self):
calc_settings = None
while True:
ok = self.exec_()
if ok != QtWidgets.QDialog.Accepted:
break
try:
cutoff_radii = self.radii_widget.cutoff_radii
surface_based = self.surf_check.isChecked()
center_based = self.center_check.isChecked()
gyration_tensor = self.gyration_tensor_check.isChecked()
overwrite = self.overwrite_check.isChecked()
exporthdf5 = self.exporthdf5_check.isChecked()
exporttext = self.exporttext_check.isChecked()
if self.exportdir_radio_config.isChecked():
exportdir = os.path.expanduser(config.Path.result_dir)
else:
exportdir = None
calc_settings = calculation.CalculationSettings(datasets=self.file_frame_dict,
resolution=self.resolution,
cutoff_radii=cutoff_radii,
domains=True,
surface_cavities=surface_based,
center_cavities=center_based,
gyration_tensor=gyration_tensor,
recalculate=overwrite,
exporthdf5=exporthdf5,
exporttext=exporttext,
exportdir=exportdir)
break
except ValueError:
pass
return (calc_settings, ok)