def _setup_table_widget(self):
"""
Make a table showing
:return: A QTableWidget object which will contain plot widgets
"""
table_widget = QTableWidget(3, 7, self)
table_widget.setVerticalHeaderLabels(['u1', 'u2', 'u3'])
col_headers = [
'a*', 'b*', 'c*'
] if self.frame == SpecialCoordinateSystem.HKL else ['Qx', 'Qy', 'Qz']
col_headers.extend(['start', 'stop', 'nbins', 'step'])
table_widget.setHorizontalHeaderLabels(col_headers)
table_widget.setFixedHeight(
table_widget.verticalHeader().defaultSectionSize() *
(table_widget.rowCount() + 1)) # +1 to include headers
for icol in range(table_widget.columnCount()):
table_widget.setColumnWidth(icol, 50)
table_widget.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
table_widget.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.table = table_widget
self.layout.addWidget(self.table)
class PMGTableShow(BaseExtendedWidget):
default_bg = QTableWidgetItem().background()
default_fg = QTableWidgetItem().foreground()
def __init__(self,
layout_dir: str,
title: List[str],
initial_value: List[List[Union[int, float, str]]],
size_restricted=False,
header_adaption_h=False,
header_adaption_v=False,
background_color: List[List[Union[str]]] = None,
foreground_color: List[List[Union[str]]] = None):
super().__init__(layout_dir=layout_dir)
self.maximum_rows = 100
self.size_restricted = size_restricted
self.header_adaption_h = header_adaption_h
self.header_adaption_v = header_adaption_v
self.background_color = background_color if background_color is not None else ''
self.foreground_color = foreground_color if foreground_color is not None else ''
self.char_width = 15
self.on_check_callback = None
self.title_list = title
entryLayout = QHBoxLayout()
entryLayout.setContentsMargins(0, 0, 0, 0)
self.ctrl = QTableWidget()
self.ctrl.verticalHeader().setVisible(False)
self.set_params(size_restricted, header_adaption_h, header_adaption_v)
self.ctrl.setColumnCount(len(title))
self.ctrl.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
for i, text in enumerate(title):
self.ctrl.setColumnWidth(i, len(text) * self.char_width + 10)
self.ctrl.setHorizontalHeaderItem(i, QTableWidgetItem(text))
self.central_layout.addLayout(entryLayout)
entryLayout.addWidget(self.ctrl)
if initial_value is not None:
for sublist in initial_value:
assert len(sublist) == len(title), \
'title is not as long as sublist,%s,%s' % (repr(title), sublist)
self.ctrl.setRowCount(len(initial_value))
self.set_value(initial_value)
def set_params(self,
size_restricted=False,
header_adaption_h=False,
header_adaption_v=False):
self.size_restricted = size_restricted
self.header_adaption_h = header_adaption_h
self.header_adaption_v = header_adaption_v
if header_adaption_h:
self.ctrl.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
if header_adaption_v:
self.ctrl.verticalHeader().setSectionResizeMode(
QHeaderView.Stretch)
def check_data(self, value: List[List[Union[int, float, str]]]):
for sublist in value:
assert len(sublist) == len(self.title_list),\
'%s,%s' % (repr(sublist), repr(self.title_list))
def set_value(self, value: List[List[Union[int, float, str]]]):
self.check_data(value)
self.ctrl.setRowCount(len(value))
cols = len(value[0])
if isinstance(self.foreground_color, str):
fg = [[self.foreground_color for i in range(cols)]
for j in range(len(value))]
else:
fg = self.foreground_color
if isinstance(self.background_color, str):
bg = [[self.background_color for i in range(cols)]
for j in range(len(value))]
else:
bg = self.background_color
for row, row_list in enumerate(value):
for col, content in enumerate(row_list):
if len(str(content)) * self.char_width > self.ctrl.columnWidth(
col):
self.ctrl.setColumnWidth(
col,
len(str(content)) * self.char_width + 10)
table_item = QTableWidgetItem(str(content))
table_item.setTextAlignment(Qt.AlignCenter)
# 字体颜色（红色）
if fg[row][col] == '':
table_item.setForeground(self.default_fg)
else:
table_item.setForeground(
QBrush(QColor(*color_str2tup(fg[row][col]))))
# 背景颜色（红色）
if bg[row][col] == '':
table_item.setBackground(self.default_bg)
else:
table_item.setBackground(
QBrush(QColor(*color_str2tup(bg[row][col]))))
self.ctrl.setItem(row, col, table_item)
if self.size_restricted:
if self.header_adaption_h:
self.ctrl.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
scrollbar_area_width = 0
else:
self.ctrl.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
scrollbar_area_width = 10
self.ctrl.setMaximumHeight((self.ctrl.rowCount() + 1) * 30 +
scrollbar_area_width)
self.setMaximumHeight((self.ctrl.rowCount() + 1) * 30 +
scrollbar_area_width)
def alert(self, alert_level: int):
self.ctrl.alert(alert_level)
def add_row(self, row: List):
assert len(row) == self.ctrl.columnCount()
rc = self.ctrl.rowCount()
self.ctrl.setRowCount(rc + 1)
for i, val in enumerate(row):
self.ctrl.setItem(rc, i, QTableWidgetItem(str(val)))
if self.ctrl.rowCount() > self.maximum_rows:
self.ctrl.removeRow(0)
class GroupsPostView(QDialog):
"""
+------------------------+
| Groups : Post/Delete |
+------------------------+
| |
| check1 Name1 |
| check2 Name2 |
| check3 Name3 |
| |
| SetAsMain |
| Apply OK Close |
+------------------------+
"""
def __init__(self, data, win_parent=None):
self.win_parent = win_parent
#Init the base class
groups = data['groups']
inames = data['inames']
self.imain = data['imain']
self.names = [group.name for group in groups]
self.white = (255, 255, 255)
self.light_grey = (211, 211, 211)
self.inames = inames
self.shown_set = data['shown']
self.deleted_groups = set()
#self.inames = argsort(self.names)
#print('inames =', inames)
anames = array(self.names)
for iname, name in enumerate(anames[self.inames]):
print('name[%s] = %r' % (iname, name))
# ignore these...
#self._default_name = data['name']
#self._default_coords = data['coords']
#self._default_elements = data['elements']
#self._default_color = data['color']
#self.coords_pound = data['coords_pound']
#self.elements_pound = data['elements_pound']
#self._default_is_discrete = data['is_discrete']
self.out_data = data
QDialog.__init__(self, win_parent)
#self.setupUi(self)
self.setWindowTitle('Groups: Post/View')
self.create_widgets()
self.create_layout()
self.set_connections()
#self.show()
def create_widgets(self):
# main/delete/supergroup
self.set_as_main_button = QPushButton("Set As Main")
self.create_super_group_button = QPushButton("Create Super Group")
self.delete_groups_button = QPushButton("Delete Groups")
self.revert_groups_button = QPushButton("Revert Groups")
self.show_groups_button = QPushButton("Show Groups")
self.hide_groups_button = QPushButton("Hide Groups")
# closing
self.apply_button = QPushButton("Apply")
self.ok_button = QPushButton("OK")
self.cancel_button = QPushButton("Cancel")
#table
self.table = QTableWidget()
self.checks = []
self.names_text = []
bold = QtGui.QFont()
bold.setBold(True)
bold.setItalic(True)
bold.setWeight(75)
anames = array(self.names)
for iname, name in enumerate(anames[self.inames]):
check = QTableWidgetItem()
check.setCheckState(False)
# TODO: create right click menu ???
name_text = QTableWidgetItem(str(name))
if iname == self.imain:
name_text.setFont(bold)
self.shown_set.add(iname)
check.setCheckState(2)
name_text.setBackground(QtGui.QColor(*self.light_grey))
elif iname in self.shown_set:
name_text.setBackground(QtGui.QColor(*self.light_grey))
self.checks.append(check)
self.names_text.append(name_text)
def create_layout(self):
nrows = len(self.names)
table = self.table
table.setRowCount(nrows)
table.setColumnCount(2)
headers = [QString('Operate On'), QString('Name')]
table.setHorizontalHeaderLabels(headers)
header = table.horizontalHeader()
header.setStretchLastSection(True)
#table.setAlternatingRowColors(True)
#header = table.verticalHeader()
#header.setStretchLastSection(True)
#table.resize(400, 250)
#heighti = table.rowHeight(0)
#total_height = nrows * heighti
#table.setMaximumHeight(total_height)
#table.resize(total_height, None)
#for iname, name in enumerate(self.names[self.inames]):
#print('name[%s] = %r' % (iname, name))
for iname in self.inames:
check = self.checks[iname]
name_text = self.names_text[iname]
# row, col, value
table.setItem(iname, 0, check)
table.setItem(iname, 1, name_text)
table.resizeRowsToContents()
#table.horizontalHeaderItem(1).setTextAlignment(QtCore.AlignHCenter)
#= QVBoxLayout()
ok_cancel_box = QHBoxLayout()
ok_cancel_box.addWidget(self.apply_button)
ok_cancel_box.addWidget(self.ok_button)
ok_cancel_box.addWidget(self.cancel_button)
vbox = QVBoxLayout()
vbox.addWidget(table)
vbox.addWidget(self.set_as_main_button)
#vbox.addWidget(self.create_super_group_button)
vbox.addStretch()
vbox.addWidget(self.show_groups_button)
vbox.addWidget(self.hide_groups_button)
vbox.addStretch()
vbox.addWidget(self.delete_groups_button)
vbox.addWidget(self.revert_groups_button)
vbox.addStretch()
vbox.addStretch()
vbox.addLayout(ok_cancel_box)
self.setLayout(vbox)
def set_connections(self):
"""creates the actions for the menu"""
self.set_as_main_button.clicked.connect(self.on_set_as_main)
self.delete_groups_button.clicked.connect(self.on_delete_groups)
self.revert_groups_button.clicked.connect(self.on_revert_groups)
self.show_groups_button.clicked.connect(self.on_show_groups)
self.hide_groups_button.clicked.connect(self.on_hide_groups)
self.create_super_group_button.clicked.connect(
self.on_create_super_group)
self.apply_button.clicked.connect(self.on_apply)
self.ok_button.clicked.connect(self.on_ok)
self.cancel_button.clicked.connect(self.on_cancel)
def closeEvent(self, event):
event.accept()
@property
def nrows(self):
return self.table.rowCount()
def on_hide_groups(self):
self._set_highlight(self.white)
def on_show_groups(self):
self._set_highlight(self.light_grey)
def _set_highlight(self, color):
for irow in range(self.nrows):
check = self.checks[irow]
is_checked = check.checkState()
# 0 - unchecked
# 1 - partially checked (invalid)
# 2 - checked
if is_checked:
name_text = self.names_text[irow]
name_text.setBackground(QtGui.QColor(*color))
def on_delete_groups(self):
for irow in range(self.nrows):
check = self.checks[irow]
is_checked = check.checkState()
# 0 - unchecked
# 1 - partially checked (invalid)
# 2 - checked
if irow == 0 and is_checked:
# TODO: change this to a log
print('error deleting group ALL...change this to a log')
#self.window_parent.log
return
if is_checked:
self.table.hideRow(irow)
self.deleted_groups.add(irow)
check.setCheckState(0)
if self.imain > 0 and self.shown_set == set([0]):
bold = QtGui.QFont()
bold.setBold(True)
bold.setItalic(True)
self.imain = 0
irow = 0
check = self.checks[irow]
name_text = self.names_texts[irow]
name_text.setFont(bold)
name_text.setBackground(QtGui.QColor(*self.light_grey))
def on_revert_groups(self):
for irow in range(self.nrows):
self.table.showRow(irow)
self.deleted_groups = set()
def on_create_super_group(self):
inames = [
iname for iname, check in enumerate(self.checks)
if bool(check.checkState())
]
if not len(inames):
# TODO: add logging
print('nothing is checked...')
return
if inames[0] == 0:
# TODO: add logging
print("cannot include 'ALL' in supergroup...")
return
name = 'SuperGroup'
# popup gui and get a name
irow = self.table.rowCount()
self.table.insertRow(irow)
check = QTableWidgetItem()
check.setCheckState(False)
name_text = QTableWidgetItem(str(name))
self.names.extend(name)
self.names_text.append(name_text)
self.checks.append(check)
self.table.setItem(irow, 0, check)
self.table.setItem(irow, 1, name_text)
def on_set_as_main(self):
bold = QtGui.QFont()
bold.setBold(True)
bold.setItalic(True)
normal = QtGui.QFont()
normal.setBold(False)
normal.setItalic(False)
imain = None
imain_set = False
for irow in range(self.nrows):
check = self.checks[irow]
name_text = self.names_text[irow]
is_checked = check.checkState()
# 0 - unchecked
# 1 - partially checked (invalid)
# 2 - checked
if is_checked and not imain_set:
# TODO: change this to a log
#self.window_parent.log
imain_set = True
imain = irow
name_text.setFont(bold)
name_text.setBackground(QtGui.QColor(*self.light_grey))
self.shown_set.add(irow)
elif irow == self.imain:
name_text.setFont(normal)
if irow == 0:
name_text.setBackground(QtGui.QColor(*self.white))
if irow in self.shown_set:
self.shown_set.remove(irow)
elif imain == 0:
name_text.setBackground(QtGui.QColor(*self.white))
self.shown_set.remove(imain)
self.imain = imain
def get_main_group(self):
return self.imain
def get_shown_group(self):
return self.shown_set
def get_deleted_groups(self):
return self.deleted_groups
def on_validate(self):
flag0 = flag1 = flag2 = True
main_group_id = self.get_main_group()
shown_groups_ids = self.get_shown_group()
deleted_group_ids = self.get_deleted_groups()
if flag0 and flag1 and flag2:
self.out_data['imain'] = main_group_id
self.out_data['shown'] = shown_groups_ids
self.out_data['remove'] = deleted_group_ids
self.out_data['clicked_ok'] = True
return True
return False
def on_apply(self):
passed = self.on_validate()
if passed:
self.win_parent.on_post_group(self.out_data)
def on_ok(self):
passed = self.on_validate()
if passed:
self.close()
#self.destroy()
def on_cancel(self):
self.close()
class CameraWindow(PyDialog):
"""defines the CameraWindow class"""
def __init__(self, data, win_parent=None):
"""
+--------+
| Camera |
+--------+---------------+
| Camera Name |
| +-------------------+ |
| | | |
| | | |
| | | |
| | | |
| | | |
| +-------------------+ |
| |
| Name xxx Save |
| Delete Set |
| |
| Apply OK Cancel |
+--------+---------------+
"""
PyDialog.__init__(self, data, win_parent)
self.setWindowTitle('Camera Views')
#self.setWindowIcon(view_icon)
self._default_name = 'Camera'
self.out_data['clicked_ok'] = False
self.cameras = deepcopy(data['cameras'])
self.names = sorted(self.cameras.keys())
self.name = QLabel("Name:")
self.name_edit = QLineEdit(str(self._default_name))
self.delete_button = QPushButton("Delete")
self.set_button = QPushButton("Set")
self.save_button = QPushButton("Save")
# closing
self.apply_button = QPushButton("Apply")
self.close_button = QPushButton("Close")
self.cancel_button = QPushButton("Cancel")
self.table = QTableWidget()
names_text = []
for name in self.names:
name_text = QTableWidgetItem(str(name))
names_text.append(name_text)
self.create_layout(names_text)
self.set_connections()
def create_layout(self, names_text):
nrows = len(self.names)
table = self.table
table.setRowCount(nrows)
table.setColumnCount(1)
headers = ['Camera Name']
table.setHorizontalHeaderLabels(headers)
header = table.horizontalHeader()
header.setStretchLastSection(True)
for iname, name_text in enumerate(names_text):
# row, col, value
table.setItem(iname, 0, name_text)
table.resizeRowsToContents()
ok_cancel_box = QHBoxLayout()
ok_cancel_box.addWidget(self.apply_button)
ok_cancel_box.addWidget(self.close_button)
ok_cancel_box.addWidget(self.cancel_button)
grid = QGridLayout()
irow = 0
grid.addWidget(self.name, irow, 0)
grid.addWidget(self.name_edit, irow, 1)
grid.addWidget(self.save_button, irow, 2)
irow += 1
grid.addWidget(self.delete_button, irow, 0)
grid.addWidget(self.set_button, irow, 1)
irow += 1
vbox = QVBoxLayout()
vbox.addWidget(self.table)
vbox.addLayout(grid)
vbox.addStretch()
vbox.addLayout(ok_cancel_box)
self.setLayout(vbox)
def set_connections(self):
"""creates the actions for the menu"""
#if qt_version == 4:
#self.connect(self.ok_button, QtCore.SIGNAL('clicked()'), self.on_ok)
self.set_button.clicked.connect(self.on_set)
self.save_button.clicked.connect(self.on_save)
self.delete_button.clicked.connect(self.on_delete)
self.apply_button.clicked.connect(self.on_apply)
self.close_button.clicked.connect(self.on_close)
self.cancel_button.clicked.connect(self.on_cancel)
def on_set(self):
objs = self.table.selectedIndexes()
if len(objs) == 1:
obj = objs[0]
irow = obj.row()
name = self.names[irow]
self.set_camera(name)
return True
return False
def on_save(self):
name = str(self.name_edit.text()).strip()
if name in self.cameras:
return
irow = self.nrows
if len(name):
self.table.insertRow(irow)
name_text = QTableWidgetItem(str(name))
self.table.setItem(irow, 0, name_text)
self.name_edit.setText('')
self.save_camera(name)
def set_camera(self, name):
camera_data = self.cameras[name]
if self.win_parent is None:
return
self.win_parent.on_set_camera_data(camera_data)
def save_camera(self, name):
self.names.append(name)
if self.win_parent is None:
self.cameras[name] = None
return
self.cameras[name] = self.win_parent.get_camera_data()
@property
def nrows(self):
return self.table.rowCount()
def on_delete(self):
irows = []
for obj in self.table.selectedIndexes():
irow = obj.row()
irows.append(irow)
irows.sort()
for irow in reversed(irows):
self.table.removeRow(irow)
name = self.names.pop(irow)
del self.cameras[name]
#print(' removing irow=%s name=%r' % (irow, name))
def closeEvent(self, event):
event.accept()
def on_apply(self):
passed = self.on_set()
#if passed:
# self.win_parent.create_plane(self.out_data)
return passed
def on_close(self):
self.out_data['clicked_ok'] = True
self.out_data['cameras'] = self.cameras
self.close()
def on_ok(self):
passed = self.on_apply()
if passed:
name = str(self.name_edit.text()).strip()
self.out_data['name'] = name
self.out_data['cameras'] = self.cameras
self.out_data['clicked_ok'] = True
self.close()
#self.destroy()
def on_cancel(self):
self.close()
class MCSDialog(QDialog):
"""A dialog to perform minimal cut set computation"""
def __init__(self, appdata: CnaData, centralwidget):
QDialog.__init__(self)
self.setWindowTitle("Minimal Cut Sets Computation")
self.appdata = appdata
self.centralwidget = centralwidget
self.eng = appdata.engine
self.out = io.StringIO()
self.err = io.StringIO()
self.layout = QVBoxLayout()
l1 = QLabel("Target Region(s)")
self.layout.addWidget(l1)
s1 = QHBoxLayout()
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
self.target_list = QTableWidget(1, 4)
self.target_list.setHorizontalHeaderLabels(
["region no", "T", "≥/≤", "t"])
self.target_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.target_list.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self.target_list.horizontalHeader().resizeSection(0, 100)
self.target_list.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
self.target_list.horizontalHeader().resizeSection(2, 50)
item = QLineEdit("1")
self.target_list.setCellWidget(0, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.target_list.setCellWidget(0, 1, item2)
combo = QComboBox(self.target_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.target_list.setCellWidget(0, 2, combo)
item = QLineEdit("0")
self.target_list.setCellWidget(0, 3, item)
s1.addWidget(self.target_list)
s11 = QVBoxLayout()
self.add_target = QPushButton("+")
self.add_target.clicked.connect(self.add_target_region)
self.rem_target = QPushButton("-")
self.rem_target.clicked.connect(self.rem_target_region)
s11.addWidget(self.add_target)
s11.addWidget(self.rem_target)
s1.addItem(s11)
self.layout.addItem(s1)
l2 = QLabel("Desired Region(s)")
self.layout.addWidget(l2)
s2 = QHBoxLayout()
self.desired_list = QTableWidget(1, 4)
self.desired_list.setHorizontalHeaderLabels(
["region no", "D", "≥/≤", "d"])
self.desired_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.desired_list.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self.desired_list.horizontalHeader().resizeSection(0, 100)
self.desired_list.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
self.desired_list.horizontalHeader().resizeSection(2, 50)
item = QLineEdit("1")
self.desired_list.setCellWidget(0, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.desired_list.setCellWidget(0, 1, item2)
combo = QComboBox(self.desired_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.desired_list.setCellWidget(0, 2, combo)
item = QLineEdit("0")
self.desired_list.setCellWidget(0, 3, item)
s2.addWidget(self.desired_list)
s21 = QVBoxLayout()
self.add_desire = QPushButton("+")
self.add_desire.clicked.connect(self.add_desired_region)
self.rem_desire = QPushButton("-")
self.rem_desire.clicked.connect(self.rem_desired_region)
s21.addWidget(self.add_desire)
s21.addWidget(self.rem_desire)
s2.addItem(s21)
self.layout.addItem(s2)
s3 = QHBoxLayout()
sgx = QVBoxLayout()
self.gen_kos = QCheckBox("Gene KOs")
self.exclude_boundary = QCheckBox(
"Exclude boundary\nreactions as cuts")
sg1 = QHBoxLayout()
s31 = QVBoxLayout()
l = QLabel("Max. Solutions")
s31.addWidget(l)
l = QLabel("Max. Size")
s31.addWidget(l)
l = QLabel("Time Limit [sec]")
s31.addWidget(l)
sg1.addItem(s31)
s32 = QVBoxLayout()
self.max_solu = QLineEdit("inf")
self.max_solu.setMaximumWidth(50)
s32.addWidget(self.max_solu)
self.max_size = QLineEdit("7")
self.max_size.setMaximumWidth(50)
s32.addWidget(self.max_size)
self.time_limit = QLineEdit("inf")
self.time_limit.setMaximumWidth(50)
s32.addWidget(self.time_limit)
sg1.addItem(s32)
sgx.addWidget(self.gen_kos)
sgx.addWidget(self.exclude_boundary)
sgx.addItem(sg1)
s3.addItem(sgx)
g3 = QGroupBox("Solver")
s33 = QVBoxLayout()
self.bg1 = QButtonGroup()
optlang_solver_name = interface_to_str(
appdata.project.cobra_py_model.problem)
self.solver_optlang = QRadioButton(f"{optlang_solver_name} (optlang)")
self.solver_optlang.setToolTip(
"Uses the solver specified by the current model.")
s33.addWidget(self.solver_optlang)
self.bg1.addButton(self.solver_optlang)
self.solver_cplex_matlab = QRadioButton("CPLEX (MATLAB)")
self.solver_cplex_matlab.setToolTip(
"Only enabled with MATLAB and CPLEX")
s33.addWidget(self.solver_cplex_matlab)
self.bg1.addButton(self.solver_cplex_matlab)
self.solver_cplex_java = QRadioButton("CPLEX (Octave)")
self.solver_cplex_java.setToolTip("Only enabled with Octave and CPLEX")
s33.addWidget(self.solver_cplex_java)
self.bg1.addButton(self.solver_cplex_java)
self.solver_intlinprog = QRadioButton("intlinprog (MATLAB)")
self.solver_intlinprog.setToolTip("Only enabled with MATLAB")
s33.addWidget(self.solver_intlinprog)
self.bg1.addButton(self.solver_intlinprog)
self.solver_glpk = QRadioButton("GLPK (Octave/MATLAB)")
s33.addWidget(self.solver_glpk)
self.bg1.addButton(self.solver_glpk)
self.bg1.buttonClicked.connect(self.configure_solver_options)
g3.setLayout(s33)
s3.addWidget(g3)
g4 = QGroupBox("MCS search")
s34 = QVBoxLayout()
self.bg2 = QButtonGroup()
self.any_mcs = QRadioButton("any MCS (fast)")
self.any_mcs.setChecked(True)
s34.addWidget(self.any_mcs)
self.bg2.addButton(self.any_mcs)
# Search type: by cardinality only with CPLEX possible
self.mcs_by_cardinality = QRadioButton("by cardinality")
s34.addWidget(self.mcs_by_cardinality)
self.bg2.addButton(self.mcs_by_cardinality)
self.smalles_mcs_first = QRadioButton("smallest MCS first")
s34.addWidget(self.smalles_mcs_first)
self.bg2.addButton(self.smalles_mcs_first)
g4.setLayout(s34)
s3.addWidget(g4)
self.layout.addItem(s3)
# Disable incompatible combinations
if appdata.selected_engine == 'None':
self.solver_optlang.setChecked(True)
self.solver_cplex_matlab.setEnabled(False)
self.solver_cplex_java.setEnabled(False)
self.solver_glpk.setEnabled(False)
self.solver_intlinprog.setEnabled(False)
if optlang_solver_name != 'cplex':
self.mcs_by_cardinality.setEnabled(False)
else:
self.solver_glpk.setChecked(True)
if not self.eng.is_cplex_matlab_ready():
self.solver_cplex_matlab.setEnabled(False)
if not self.eng.is_cplex_java_ready():
self.solver_cplex_java.setEnabled(False)
if self.appdata.is_matlab_set():
self.solver_cplex_java.setEnabled(False)
if not self.appdata.is_matlab_set():
self.solver_cplex_matlab.setEnabled(False)
self.solver_intlinprog.setEnabled(False)
self.configure_solver_options()
s4 = QVBoxLayout()
self.consider_scenario = QCheckBox(
"Consider constraint given by scenario")
s4.addWidget(self.consider_scenario)
self.advanced = QCheckBox(
"Advanced: Define knockout/addition costs for genes/reactions")
self.advanced.setEnabled(False)
s4.addWidget(self.advanced)
self.layout.addItem(s4)
buttons = QHBoxLayout()
# self.save = QPushButton("save")
# buttons.addWidget(self.save)
# self.load = QPushButton("load")
# buttons.addWidget(self.load)
self.compute_mcs = QPushButton("Compute MCS")
buttons.addWidget(self.compute_mcs)
# self.compute_mcs2 = QPushButton("Compute MCS2")
# buttons.addWidget(self.compute_mcs2)
self.cancel = QPushButton("Close")
buttons.addWidget(self.cancel)
self.layout.addItem(buttons)
# max width for buttons
self.add_target.setMaximumWidth(20)
self.rem_target.setMaximumWidth(20)
self.add_desire.setMaximumWidth(20)
self.rem_desire.setMaximumWidth(20)
self.setLayout(self.layout)
# Connecting the signal
self.cancel.clicked.connect(self.reject)
self.compute_mcs.clicked.connect(self.compute)
@Slot()
def configure_solver_options(self):
optlang_solver_name = interface_to_str(
self.appdata.project.cobra_py_model.problem)
if self.solver_optlang.isChecked():
self.gen_kos.setChecked(False)
self.gen_kos.setEnabled(False)
self.exclude_boundary.setEnabled(True)
if optlang_solver_name != 'cplex':
if self.mcs_by_cardinality.isChecked():
self.mcs_by_cardinality.setChecked(False)
self.any_mcs.setChecked(True)
self.mcs_by_cardinality.setEnabled(False)
self.mcs_by_cardinality.setChecked(False)
else:
self.gen_kos.setEnabled(True)
self.exclude_boundary.setChecked(False)
self.exclude_boundary.setEnabled(False)
self.mcs_by_cardinality.setEnabled(True)
def add_target_region(self):
i = self.target_list.rowCount()
self.target_list.insertRow(i)
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
item = QLineEdit("1")
self.target_list.setCellWidget(i, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.target_list.setCellWidget(i, 1, item2)
combo = QComboBox(self.target_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.target_list.setCellWidget(i, 2, combo)
item = QLineEdit("0")
self.target_list.setCellWidget(i, 3, item)
def add_desired_region(self):
i = self.desired_list.rowCount()
self.desired_list.insertRow(i)
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
item = QLineEdit("1")
self.desired_list.setCellWidget(i, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.desired_list.setCellWidget(i, 1, item2)
combo = QComboBox(self.desired_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.desired_list.setCellWidget(i, 2, combo)
item = QLineEdit("0")
self.desired_list.setCellWidget(i, 3, item)
def rem_target_region(self):
i = self.target_list.rowCount()
self.target_list.removeRow(i-1)
def rem_desired_region(self):
i = self.desired_list.rowCount()
self.desired_list.removeRow(i-1)
def compute(self):
if self.solver_optlang.isChecked():
self.compute_optlang()
else:
self.compute_legacy()
def compute_legacy(self):
self.setCursor(Qt.BusyCursor)
# create CobraModel for matlab
with self.appdata.project.cobra_py_model as model:
if self.consider_scenario.isChecked(): # integrate scenario into model bounds
for r in self.appdata.project.scen_values.keys():
model.reactions.get_by_id(
r).bounds = self.appdata.project.scen_values[r]
cobra.io.save_matlab_model(model, os.path.join(
self.appdata.cna_path, "cobra_model.mat"), varname="cbmodel")
self.eng.eval("load('cobra_model.mat')",
nargout=0)
try:
self.eng.eval("cnap = CNAcobra2cna(cbmodel);",
nargout=0,
stdout=self.out, stderr=self.err)
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'Unknown exception occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return
self.eng.eval("genes = [];", nargout=0,
stdout=self.out, stderr=self.err)
cmd = "maxSolutions = " + str(float(self.max_solu.text())) + ";"
self.eng.eval(cmd, nargout=0, stdout=self.out, stderr=self.err)
cmd = "maxSize = " + str(int(self.max_size.text())) + ";"
self.eng.eval(cmd, nargout=0, stdout=self.out, stderr=self.err)
cmd = "milp_time_limit = " + str(float(self.time_limit.text())) + ";"
self.eng.eval(cmd, nargout=0, stdout=self.out, stderr=self.err)
if self.gen_kos.isChecked():
self.eng.eval("gKOs = 1;", nargout=0)
else:
self.eng.eval("gKOs = 0;", nargout=0)
if self.advanced.isChecked():
self.eng.eval("advanced_on = 1;", nargout=0)
else:
self.eng.eval("advanced_on = 0;", nargout=0)
if self.solver_intlinprog.isChecked():
self.eng.eval("solver = 'intlinprog';", nargout=0)
if self.solver_cplex_java.isChecked():
self.eng.eval("solver = 'java_cplex_new';", nargout=0)
if self.solver_cplex_matlab.isChecked():
self.eng.eval("solver = 'matlab_cplex';", nargout=0)
if self.solver_glpk.isChecked():
self.eng.eval("solver = 'glpk';", nargout=0)
if self.any_mcs.isChecked():
self.eng.eval("mcs_search_mode = 'search_1';", nargout=0)
elif self.mcs_by_cardinality.isChecked():
self.eng.eval("mcs_search_mode = 'search_2';", nargout=0)
elif self.smalles_mcs_first.isChecked():
self.eng.eval("mcs_search_mode = 'search_3';", nargout=0)
rows = self.target_list.rowCount()
for i in range(0, rows):
p1 = self.target_list.cellWidget(i, 0).text()
p2 = self.target_list.cellWidget(i, 1).text()
if self.target_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = self.target_list.cellWidget(i, 3).text()
cmd = "dg_T = {[" + p1+"], '" + p2 + \
"', '" + p3 + "', [" + p4 + "']};"
self.eng.eval(cmd, nargout=0,
stdout=self.out, stderr=self.err)
rows = self.desired_list.rowCount()
for i in range(0, rows):
p1 = self.desired_list.cellWidget(i, 0).text()
p2 = self.desired_list.cellWidget(i, 1).text()
if self.desired_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = self.desired_list.cellWidget(i, 3).text()
cmd = "dg_D = {[" + p1+"], '" + p2 + \
"', '" + p3 + "', [" + p4 + "']};"
self.eng.eval(cmd, nargout=0)
# get some data
self.eng.eval("reac_id = cellstr(cnap.reacID).';",
nargout=0, stdout=self.out, stderr=self.err)
mcs = []
values = []
reactions = []
reac_id = []
if self.appdata.is_matlab_set():
reac_id = self.eng.workspace['reac_id']
try:
self.eng.eval("[mcs] = cnapy_compute_mcs(cnap, genes, maxSolutions, maxSize, milp_time_limit, gKOs, advanced_on, solver, mcs_search_mode, dg_T,dg_D);",
nargout=0)
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'Unknown exception occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return
else:
self.eng.eval("[reaction, mcs, value] = find(mcs);", nargout=0,
stdout=self.out, stderr=self.err)
reactions = self.eng.workspace['reaction']
mcs = self.eng.workspace['mcs']
values = self.eng.workspace['value']
elif self.appdata.is_octave_ready():
reac_id = self.eng.pull('reac_id')
reac_id = reac_id[0]
try:
self.eng.eval("[mcs] = cnapy_compute_mcs(cnap, genes, maxSolutions, maxSize, milp_time_limit, gKOs, advanced_on, solver, mcs_search_mode, dg_T,dg_D);",
nargout=0)
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'Unknown exception occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return
else:
self.eng.eval("[reaction, mcs, value] = find(mcs);", nargout=0,
stdout=self.out, stderr=self.err)
reactions = self.eng.pull('reaction')
mcs = self.eng.pull('mcs')
values = self.eng.pull('value')
if len(mcs) == 0:
QMessageBox.information(self, 'No cut sets',
'Cut sets have not been calculated or do not exist.')
else:
last_mcs = 1
omcs = []
current_mcs = {}
for i in range(0, len(reactions)):
reacid = int(reactions[i][0])
reaction = reac_id[reacid-1]
c_mcs = int(mcs[i][0])
c_value = int(values[i][0])
if c_value == -1: # -1 stands for removed which is 0 in the ui
c_value = 0
if c_mcs > last_mcs:
omcs.append(current_mcs)
last_mcs = c_mcs
current_mcs = {}
current_mcs[reaction] = c_value
omcs.append(current_mcs)
self.appdata.project.modes = omcs
self.centralwidget.mode_navigator.current = 0
QMessageBox.information(self, 'Cut sets found',
str(len(omcs))+' Cut sets have been calculated.')
self.centralwidget.update_mode()
self.centralwidget.mode_navigator.title.setText("MCS Navigation")
self.setCursor(Qt.ArrowCursor)
def compute_optlang(self):
self.setCursor(Qt.BusyCursor)
max_mcs_num = float(self.max_solu.text())
max_mcs_size = int(self.max_size.text())
timeout = float(self.time_limit.text())
if timeout is float('inf'):
timeout = None
# if self.gen_kos.isChecked():
# self.eng.eval("gKOs = 1;", nargout=0)
# else:
# self.eng.eval("gKOs = 0;", nargout=0)
# if self.advanced.isChecked():
# self.eng.eval("advanced_on = 1;", nargout=0)
# else:
# self.eng.eval("advanced_on = 0;", nargout=0)
if self.smalles_mcs_first.isChecked():
enum_method = 1
elif self.mcs_by_cardinality.isChecked():
enum_method = 2
elif self.any_mcs.isChecked():
enum_method = 3
with self.appdata.project.cobra_py_model as model:
if self.consider_scenario.isChecked(): # integrate scenario into model bounds
for r in self.appdata.project.scen_values.keys():
model.reactions.get_by_id(
r).bounds = self.appdata.project.scen_values[r]
reac_id = model.reactions.list_attr("id")
reac_id_symbols = cMCS_enumerator.get_reac_id_symbols(reac_id)
rows = self.target_list.rowCount()
targets = dict()
for i in range(0, rows):
p1 = self.target_list.cellWidget(i, 0).text()
p2 = self.target_list.cellWidget(i, 1).text()
if len(p1) > 0 and len(p2) > 0:
if self.target_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = float(self.target_list.cellWidget(i, 3).text())
targets.setdefault(p1, []).append((p2, p3, p4))
targets = list(targets.values())
targets = [cMCS_enumerator.relations2leq_matrix(cMCS_enumerator.parse_relations(
t, reac_id_symbols=reac_id_symbols), reac_id) for t in targets]
rows = self.desired_list.rowCount()
desired = dict()
for i in range(0, rows):
p1 = self.desired_list.cellWidget(i, 0).text()
p2 = self.desired_list.cellWidget(i, 1).text()
if len(p1) > 0 and len(p2) > 0:
if self.desired_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = float(self.desired_list.cellWidget(i, 3).text())
desired.setdefault(p1, []).append((p2, p3, p4))
desired = list(desired.values())
desired = [cMCS_enumerator.relations2leq_matrix(cMCS_enumerator.parse_relations(
d, reac_id_symbols=reac_id_symbols), reac_id) for d in desired]
try:
mcs = cMCS_enumerator.compute_mcs(model,
targets=targets,
desired=desired,
enum_method=enum_method,
max_mcs_size=max_mcs_size,
max_mcs_num=max_mcs_num,
timeout=timeout,
exclude_boundary_reactions_as_cuts=self.exclude_boundary.isChecked())
except cMCS_enumerator.InfeasibleRegion as e:
QMessageBox.warning(self, 'Cannot calculate MCS', str(e))
return targets, desired
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'An exception has occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return targets, desired
finally:
self.setCursor(Qt.ArrowCursor)
if len(mcs) == 0:
QMessageBox.information(self, 'No cut sets',
'Cut sets have not been calculated or do not exist.')
return targets, desired
omcs = [{reac_id[i]: 0 for i in m} for m in mcs]
self.appdata.project.modes = omcs
self.centralwidget.mode_navigator.current = 0
QMessageBox.information(self, 'Cut sets found',
str(len(omcs))+' Cut sets have been calculated.')
self.centralwidget.update_mode()
self.centralwidget.mode_navigator.title.setText("MCS Navigation")
class Extension2ReaderTable(QWidget):
"""Table showing extension to reader mappings with removal button.
Widget presented in preferences-plugin dialog."""
valueChanged = Signal(int)
def __init__(self, parent=None):
super().__init__(parent=parent)
self._table = QTableWidget()
self._table.setShowGrid(False)
self._populate_table()
layout = QVBoxLayout()
layout.addWidget(self._table)
self.setLayout(layout)
def _populate_table(self):
"""Add row for each extension to reader mapping in settings"""
self._extension_col = 0
self._reader_col = 1
header_strs = [trans._('Extension'), trans._('Reader Plugin')]
self._table.setColumnCount(2)
self._table.setColumnWidth(self._extension_col, 100)
self._table.setColumnWidth(self._reader_col, 150)
self._table.verticalHeader().setVisible(False)
self._table.setMinimumHeight(120)
extension2reader = get_settings().plugins.extension2reader
if len(extension2reader) > 0:
self._table.setRowCount(len(extension2reader))
self._table.horizontalHeader().setStretchLastSection(True)
self._table.horizontalHeader().setStyleSheet(
'border-bottom: 2px solid white;')
self._table.setHorizontalHeaderLabels(header_strs)
for row, (extension,
plugin_name) in enumerate(extension2reader.items()):
item = QTableWidgetItem(extension)
item.setFlags(Qt.NoItemFlags)
self._table.setItem(row, self._extension_col, item)
plugin_widg = QWidget()
# need object name to easily find row
plugin_widg.setObjectName(f'{extension}')
plugin_widg.setLayout(QHBoxLayout())
plugin_widg.layout().setContentsMargins(0, 0, 0, 0)
plugin_label = QLabel(plugin_name)
# need object name to easily work out which button was clicked
remove_btn = QPushButton('x', objectName=f'{extension}')
remove_btn.setFixedWidth(30)
remove_btn.setStyleSheet('margin: 4px;')
remove_btn.setToolTip(
trans._('Remove this extension to reader association'))
remove_btn.clicked.connect(self._remove_extension_assignment)
plugin_widg.layout().addWidget(plugin_label)
plugin_widg.layout().addWidget(remove_btn)
self._table.setCellWidget(row, self._reader_col, plugin_widg)
else:
# Display that there are no extensions with reader associations
self._table.setRowCount(1)
self._table.setHorizontalHeaderLabels(header_strs)
self._table.setColumnHidden(self._reader_col, True)
self._table.setColumnWidth(self._extension_col, 200)
item = QTableWidgetItem(trans._('No extensions found.'))
item.setFlags(Qt.NoItemFlags)
self._table.setItem(0, 0, item)
def _remove_extension_assignment(self, event):
"""Delete extension to reader mapping setting and remove table row"""
extension_to_remove = self.sender().objectName()
current_settings = get_settings().plugins.extension2reader
# need explicit assignment to new object here for persistence
get_settings().plugins.extension2reader = {
k: v
for k, v in current_settings.items() if k != extension_to_remove
}
for i in range(self._table.rowCount()):
row_widg_name = self._table.cellWidget(
i, self._reader_col).objectName()
if row_widg_name == extension_to_remove:
self._table.removeRow(i)
return
class WndManageEmissionLines(SecondaryWindow):
signal_selected_element_changed = Signal(str)
signal_update_element_selection_list = Signal()
signal_update_add_remove_btn_state = Signal(bool, bool)
signal_marker_state_changed = Signal(bool)
signal_parameters_changed = Signal()
def __init__(self, *, gpc, gui_vars):
super().__init__()
# Global processing classes
self.gpc = gpc
# Global GUI variables (used for control of GUI state)
self.gui_vars = gui_vars
# Threshold used for peak removal (displayed in lineedit)
self._remove_peak_threshold = self.gpc.get_peak_threshold()
self._enable_events = False
self._eline_list = [
] # List of emission lines (used in the line selection combo)
self._table_contents = [
] # Keep a copy of table contents (list of dict)
self._selected_eline = ""
self.initialize()
self._enable_events = True
# Marker state is reported by Matplotlib plot in 'line_plot' model
def cb(marker_state):
self.signal_marker_state_changed.emit(marker_state)
self.gpc.set_marker_reporter(cb)
self.signal_marker_state_changed.connect(
self.slot_marker_state_changed)
# Update button states
self._update_add_remove_btn_state()
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def initialize(self):
self.setWindowTitle("PyXRF: Add/Remove Emission Lines")
self.resize(600, 600)
top_buttons = self._setup_select_elines()
self._setup_elines_table()
bottom_buttons = self._setup_action_buttons()
vbox = QVBoxLayout()
# Group of buttons above the table
vbox.addLayout(top_buttons)
# Tables
hbox = QHBoxLayout()
hbox.addWidget(self.tbl_elines)
vbox.addLayout(hbox)
vbox.addLayout(bottom_buttons)
self.setLayout(vbox)
self._set_tooltips()
def _setup_select_elines(self):
self.cb_select_all = QCheckBox("All")
self.cb_select_all.setChecked(True)
self.cb_select_all.toggled.connect(self.cb_select_all_toggled)
self.element_selection = ElementSelection()
# The following field should switched to 'editable' state from when needed
self.le_peak_intensity = LineEditReadOnly()
self.pb_add_eline = QPushButton("Add")
self.pb_add_eline.clicked.connect(self.pb_add_eline_clicked)
self.pb_remove_eline = QPushButton("Remove")
self.pb_remove_eline.clicked.connect(self.pb_remove_eline_clicked)
self.pb_user_peaks = QPushButton("New User Peak ...")
self.pb_user_peaks.clicked.connect(self.pb_user_peaks_clicked)
self.pb_pileup_peaks = QPushButton("New Pileup Peak ...")
self.pb_pileup_peaks.clicked.connect(self.pb_pileup_peaks_clicked)
self.element_selection.signal_current_item_changed.connect(
self.element_selection_item_changed)
vbox = QVBoxLayout()
hbox = QHBoxLayout()
hbox.addWidget(self.element_selection)
hbox.addWidget(self.le_peak_intensity)
hbox.addWidget(self.pb_add_eline)
hbox.addWidget(self.pb_remove_eline)
vbox.addLayout(hbox)
hbox = QHBoxLayout()
hbox.addWidget(self.cb_select_all)
hbox.addStretch(1)
hbox.addWidget(self.pb_user_peaks)
hbox.addWidget(self.pb_pileup_peaks)
vbox.addLayout(hbox)
# Wrap vbox into hbox, because it will be inserted into vbox
hbox = QHBoxLayout()
hbox.addLayout(vbox)
hbox.addStretch(1)
return hbox
def _setup_elines_table(self):
"""The table has only functionality necessary to demonstrate how it is going
to look. A lot more code is needed to actually make it run."""
self._validator_peak_height = QDoubleValidator()
self._validator_peak_height.setBottom(0.01)
self.tbl_elines = QTableWidget()
self.tbl_elines.setStyleSheet(
"QTableWidget::item{color: black;}"
"QTableWidget::item:selected{background-color: red;}"
"QTableWidget::item:selected{color: white;}")
self.tbl_labels = [
"", "Z", "Line", "E, keV", "Peak Int.", "Rel. Int.(%)", "CS"
]
self.tbl_cols_editable = ["Peak Int."]
self.tbl_value_min = {"Rel. Int.(%)": 0.1}
tbl_cols_resize_to_content = ["", "Z", "Line"]
self.tbl_elines.setColumnCount(len(self.tbl_labels))
self.tbl_elines.verticalHeader().hide()
self.tbl_elines.setHorizontalHeaderLabels(self.tbl_labels)
self.tbl_elines.setSelectionBehavior(QTableWidget.SelectRows)
self.tbl_elines.setSelectionMode(QTableWidget.SingleSelection)
self.tbl_elines.itemSelectionChanged.connect(
self.tbl_elines_item_selection_changed)
self.tbl_elines.itemChanged.connect(self.tbl_elines_item_changed)
header = self.tbl_elines.horizontalHeader()
for n, lbl in enumerate(self.tbl_labels):
# Set stretching for the columns
if lbl in tbl_cols_resize_to_content:
header.setSectionResizeMode(n, QHeaderView.ResizeToContents)
else:
header.setSectionResizeMode(n, QHeaderView.Stretch)
# Set alignment for the columns headers (HEADERS only)
if n == 0:
header.setDefaultAlignment(Qt.AlignCenter)
else:
header.setDefaultAlignment(Qt.AlignRight)
self.cb_sel_list = [] # List of checkboxes
def _setup_action_buttons(self):
self.pb_remove_rel = QPushButton("Remove Rel.Int.(%) <")
self.pb_remove_rel.clicked.connect(self.pb_remove_rel_clicked)
self.le_remove_rel = LineEditExtended("")
self._validator_le_remove_rel = QDoubleValidator()
self._validator_le_remove_rel.setBottom(0.01) # Some small number
self._validator_le_remove_rel.setTop(100.0)
self.le_remove_rel.setText(
self._format_threshold(self._remove_peak_threshold))
self._update_le_remove_rel_state()
self.le_remove_rel.textChanged.connect(self.le_remove_rel_text_changed)
self.le_remove_rel.editingFinished.connect(
self.le_remove_rel_editing_finished)
self.pb_remove_unchecked = QPushButton("Remove Unchecked Lines")
self.pb_remove_unchecked.clicked.connect(
self.pb_remove_unchecked_clicked)
hbox = QHBoxLayout()
hbox.addWidget(self.pb_remove_rel)
hbox.addWidget(self.le_remove_rel)
hbox.addStretch(1)
hbox.addWidget(self.pb_remove_unchecked)
return hbox
def _set_tooltips(self):
set_tooltip(self.cb_select_all,
"<b>Select/Deselect All</b> emission lines in the list")
set_tooltip(self.element_selection, "<b>Set active</b> emission line")
set_tooltip(self.le_peak_intensity,
"Set or modify <b>intensity</b> of the active peak.")
set_tooltip(self.pb_add_eline, "<b>Add</b> emission line to the list.")
set_tooltip(self.pb_remove_eline,
"<b>Remove</b> emission line from the list.")
set_tooltip(
self.pb_user_peaks,
"Open dialog box to add or modify parameters of the <b>user-defined peak</b>"
)
set_tooltip(
self.pb_pileup_peaks,
"Open dialog box to add or modify parameters of the <b>pileup peak</b>"
)
set_tooltip(self.tbl_elines,
"The list of the selected <b>emission lines</b>")
# set_tooltip(self.pb_update,
# "Update the internally stored list of selected emission lines "
# "and their parameters. This button is <b>deprecated</b>, but still may be "
# "needed in some situations. In future releases it will be <b>removed</b> or replaced "
# "with 'Accept' button. Substantial changes to the computational code is needed before "
# "it happens.")
# set_tooltip(self.pb_undo,
# "<b>Undo</b> changes to the table of selected emission lines. Doesn't always work.")
set_tooltip(
self.pb_remove_rel,
"<b>Remove emission lines</b> from the list if their relative intensity is less "
"then specified threshold.",
)
set_tooltip(
self.le_remove_rel,
"<b>Threshold</b> that controls which emission lines are removed "
"when <b>Remove Rel.Int.(%)</b> button is pressed.",
)
set_tooltip(self.pb_remove_unchecked,
"Remove <b>unchecked</b> emission lines from the list.")
def update_widget_state(self, condition=None):
# Update the state of the menu bar
state = not self.gui_vars["gui_state"]["running_computations"]
self.setEnabled(state)
# Hide the window if required by the program state
state_file_loaded = self.gui_vars["gui_state"]["state_file_loaded"]
state_model_exist = self.gui_vars["gui_state"]["state_model_exists"]
if not state_file_loaded or not state_model_exist:
self.hide()
if condition == "tooltips":
self._set_tooltips()
def fill_eline_table(self, table_contents):
self._table_contents = copy.deepcopy(table_contents)
self._enable_events = False
self.tbl_elines.clearContents()
# Clear the list of checkboxes
for cb in self.cb_sel_list:
cb.stateChanged.connect(self.cb_eline_state_changed)
self.cb_sel_list = []
self.tbl_elines.setRowCount(len(table_contents))
for nr, row in enumerate(table_contents):
sel_status = row["sel_status"]
row_data = [
None, row["z"], row["eline"], row["energy"], row["peak_int"],
row["rel_int"], row["cs"]
]
for nc, entry in enumerate(row_data):
label = self.tbl_labels[nc]
# Set alternating background colors for the table rows
# Make background for editable items a little brighter
brightness = 240 if label in self.tbl_cols_editable else 220
if nr % 2:
rgb_bckg = (255, brightness, brightness) # Light-red
else:
rgb_bckg = (brightness, 255, brightness) # Light-green
if nc == 0:
item = QWidget()
cb = CheckBoxNamed(name=f"{nr}")
item_hbox = QHBoxLayout(item)
item_hbox.addWidget(cb)
item_hbox.setAlignment(Qt.AlignCenter)
item_hbox.setContentsMargins(0, 0, 0, 0)
css1 = get_background_css(rgb_bckg,
widget="QCheckbox",
editable=False)
css2 = get_background_css(rgb_bckg,
widget="QWidget",
editable=False)
item.setStyleSheet(css2 + css1)
cb.setChecked(Qt.Checked if sel_status else Qt.Unchecked)
cb.stateChanged.connect(self.cb_eline_state_changed)
cb.setStyleSheet("QCheckBox {color: black;}")
self.cb_sel_list.append(cb)
self.tbl_elines.setCellWidget(nr, nc, item)
else:
s = None
# The case when the value (Rel. Int.) is limited from the bottom
# We don't want to print very small numbers here
if label in self.tbl_value_min:
v = self.tbl_value_min[label]
if isinstance(entry,
(float, np.float64)) and (entry < v):
s = f"<{v:.2f}"
if s is None:
if isinstance(entry, (float, np.float64)):
s = f"{entry:.2f}" if entry else "-"
else:
s = f"{entry}" if entry else "-"
item = QTableWidgetItem(s)
item.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
# Set all columns not editable (unless needed)
if label not in self.tbl_cols_editable:
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
brush = QBrush(QColor(*rgb_bckg))
item.setBackground(brush)
self.tbl_elines.setItem(nr, nc, item)
self._enable_events = True
# Update the rest of the widgets
self._update_widgets_based_on_table_state()
@Slot()
def update_widget_data(self):
# This is typically a new set of emission lines. Clear the selection both
# in the table and in the element selection tool.
self.element_selection.set_current_item("")
self.tbl_elines.clearSelection()
self._set_selected_eline("")
# Now update the tables
self._update_eline_selection_list()
self.update_eline_table()
self._update_add_remove_btn_state()
def pb_pileup_peaks_clicked(self):
data = {}
eline = self._selected_eline
if self.gpc.get_eline_name_category(eline) == "pileup":
logger.error(
f"Attempt to add pileup peak '{eline}' while another pileup peak is selected."
)
return
energy, marker_visible = self.gpc.get_suggested_manual_peak_energy()
best_guess = self.gpc.get_guessed_pileup_peak_components(energy=energy,
tolerance=0.1)
if best_guess is not None:
el1, el2, energy = best_guess
else:
# No peaks were found, enter peaks manually
el1, el2, energy = "", "", 0
data["element1"] = el1
data["element2"] = el2
data["energy"] = energy
data["range_low"], data[
"range_high"] = self.gpc.get_selected_energy_range()
if not marker_visible:
# We shouldn't end up here, but this will protect from crashing in case
# the button was not disabled (a bug).
msg = "Select location of the new peak center (energy)\nby clicking on the plot in 'Fit Model' tab"
msgbox = QMessageBox(QMessageBox.Information,
"User Input Required",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
else:
dlg = DialogPileupPeakParameters()
def func():
def f(e1, e2):
try:
name = self.gpc.generate_pileup_peak_name(e1, e2)
e = self.gpc.get_pileup_peak_energy(name)
except Exception:
e = 0
return e
return f
dlg.set_compute_energy_function(func())
dlg.set_parameters(data)
if dlg.exec():
print("Pileup peak is added")
try:
data = dlg.get_parameters()
eline1, eline2 = data["element1"], data["element2"]
eline = self.gpc.generate_pileup_peak_name(eline1, eline2)
self.gpc.add_peak_manual(eline)
self.update_eline_table() # Update the table
self.tbl_elines_set_selection(
eline) # Select new emission line
self._set_selected_eline(eline)
self._set_fit_status(False)
logger.info(f"New pileup peak {eline} was added")
except RuntimeError as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
def pb_user_peaks_clicked(self):
eline = self._selected_eline
# If current peak is user_defined peak
is_userpeak = self.gpc.get_eline_name_category(eline) == "userpeak"
if is_userpeak:
data = {}
data["enabled"] = True
data["name"] = eline
data["maxv"] = self.gpc.get_eline_intensity(eline)
data["energy"], data[
"fwhm"] = self.gpc.get_current_userpeak_energy_fwhm()
dlg = DialogEditUserPeakParameters()
dlg.set_parameters(data=data)
if dlg.exec():
print("Editing of user defined peak is completed")
try:
eline = data["name"]
data = dlg.get_parameters()
self.gpc.update_userpeak(data["name"], data["energy"],
data["maxv"], data["fwhm"])
self._set_fit_status(False)
logger.info(f"User defined peak {eline} was updated.")
except Exception as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
else:
data = {}
data["name"] = self.gpc.get_unused_userpeak_name()
data[
"energy"], marker_visible = self.gpc.get_suggested_manual_peak_energy(
)
if marker_visible:
dlg = DialogNewUserPeak()
dlg.set_parameters(data=data)
if dlg.exec():
try:
eline = data["name"]
self.gpc.add_peak_manual(eline)
self.update_eline_table() # Update the table
self.tbl_elines_set_selection(
eline) # Select new emission line
self._set_selected_eline(eline)
self._set_fit_status(False)
logger.info(f"New user defined peak {eline} is added")
except RuntimeError as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
else:
msg = ("Select location of the new peak center (energy)\n"
"by clicking on the plot in 'Fit Model' tab")
msgbox = QMessageBox(QMessageBox.Information,
"User Input Required",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
@Slot()
def pb_add_eline_clicked(self):
logger.debug("'Add line' clicked")
# It is assumed that this button is active only if an element is selected from the list
# of available emission lines. It can't be used to add user-defined peaks or pileup peaks.
eline = self._selected_eline
if eline:
try:
self.gpc.add_peak_manual(eline)
self.update_eline_table() # Update the table
self.tbl_elines_set_selection(
eline) # Select new emission line
self._set_fit_status(False)
except RuntimeError as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
@Slot()
def pb_remove_eline_clicked(self):
logger.debug("'Remove line' clicked")
eline = self._selected_eline
if eline:
# If currently selected line is the emission line (like Ca_K), we want
# it to remain selected after it is deleted. This means that nothing is selected
# in the table. For other lines, nothing should remain selected.
self.tbl_elines.clearSelection()
self.gpc.remove_peak_manual(eline)
self.update_eline_table() # Update the table
if self.gpc.get_eline_name_category(eline) != "eline":
eline = ""
# This will update widgets
self._set_selected_eline(eline)
self._set_fit_status(False)
def cb_select_all_toggled(self, state):
self._enable_events = False
eline_list, state_list = [], []
for n_row in range(self.tbl_elines.rowCount()):
eline = self._table_contents[n_row]["eline"]
# Do not deselect lines in category 'other'. They probably never to be deleted.
# They also could be deselected manually.
if self.gpc.get_eline_name_category(
eline) == "other" and not state:
to_check = True
else:
to_check = state
self.cb_sel_list[n_row].setChecked(
Qt.Checked if to_check else Qt.Unchecked)
eline_list.append(eline)
state_list.append(to_check)
self.gpc.set_checked_emission_lines(eline_list, state_list)
self._set_fit_status(False)
self._enable_events = True
def cb_eline_state_changed(self, name, state):
if self._enable_events:
n_row = int(name)
state = state == Qt.Checked
eline = self._table_contents[n_row]["eline"]
self.gpc.set_checked_emission_lines([eline], [state])
self._set_fit_status(False)
def tbl_elines_item_changed(self, item):
if self._enable_events:
n_row, n_col = self.tbl_elines.row(item), self.tbl_elines.column(
item)
# Value was changed
if n_col == 4:
text = item.text()
eline = self._table_contents[n_row]["eline"]
if self._validator_peak_height.validate(
text, 0)[0] != QDoubleValidator.Acceptable:
val = self._table_contents[n_row]["peak_int"]
self._enable_events = False
item.setText(f"{val:.2f}")
self._enable_events = True
self._set_fit_status(False)
else:
self.gpc.update_eline_peak_height(eline, float(text))
self.update_eline_table()
def tbl_elines_item_selection_changed(self):
sel_ranges = self.tbl_elines.selectedRanges()
# The table is configured to have one or no selected ranges
# 'Open' button should be enabled only if a range (row) is selected
if sel_ranges:
index = sel_ranges[0].topRow()
eline = self._table_contents[index]["eline"]
if self._enable_events:
self._enable_events = False
self._set_selected_eline(eline)
self.element_selection.set_current_item(eline)
self._enable_events = True
def tbl_elines_set_selection(self, eline):
"""
Select the row with emission line `eline` in the table. Deselect everything if
the emission line does not exist.
"""
index = self._get_eline_index_in_table(eline)
self.tbl_elines.clearSelection()
if index >= 0:
self.tbl_elines.selectRow(index)
def element_selection_item_changed(self, index, eline):
self.signal_selected_element_changed.emit(eline)
if self._enable_events:
self._enable_events = False
self._set_selected_eline(eline)
self.tbl_elines_set_selection(eline)
self._enable_events = True
def pb_remove_rel_clicked(self):
try:
self.gpc.remove_peaks_below_threshold(self._remove_peak_threshold)
except Exception as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
self.update_eline_table()
# Update the displayed estimated peak amplitude value 'le_peak_intensity'
self._set_selected_eline(self._selected_eline)
self._set_fit_status(False)
def le_remove_rel_text_changed(self, text):
self._update_le_remove_rel_state(text)
def le_remove_rel_editing_finished(self):
text = self.le_remove_rel.text()
if self._validator_le_remove_rel.validate(
text, 0)[0] == QDoubleValidator.Acceptable:
self._remove_peak_threshold = float(text)
else:
self.le_remove_rel.setText(
self._format_threshold(self._remove_peak_threshold))
def pb_remove_unchecked_clicked(self):
try:
self.gpc.remove_unchecked_peaks()
except Exception as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table
self.update_eline_table()
# Update the displayed estimated peak amplitude value 'le_peak_intensity'
self._set_selected_eline(self._selected_eline)
self._set_fit_status(False)
def _display_peak_intensity(self, eline):
v = self.gpc.get_eline_intensity(eline)
s = f"{v:.10g}" if v is not None else ""
self.le_peak_intensity.setText(s)
def _update_le_remove_rel_state(self, text=None):
if text is None:
text = self.le_remove_rel.text()
state = self._validator_le_remove_rel.validate(
text, 0)[0] == QDoubleValidator.Acceptable
self.le_remove_rel.setValid(state)
self.pb_remove_rel.setEnabled(state)
@Slot(str)
def slot_selection_item_changed(self, eline):
self.element_selection.set_current_item(eline)
@Slot(bool)
def slot_marker_state_changed(self, state):
# If userpeak is selected and plot is clicked (marker is set), then user
# should be allowed to add userpeak at a new location. So deselect the userpeak
# from the table (if it is selected)
logger.debug(
f"Vertical marker on the fit plot changed state to {state}.")
if state:
self._deselect_special_peak_in_table()
# Now update state of all buttons
self._update_add_remove_btn_state()
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def _format_threshold(self, value):
return f"{value:.2f}"
def _deselect_special_peak_in_table(self):
"""Deselect userpeak if a userpeak is selected"""
if self.gpc.get_eline_name_category(
self._selected_eline) in ("userpeak", "pileup"):
# Clear all selections
self.tbl_elines_set_selection("")
self._set_selected_eline("")
# We also want to show marker at the new position
self.gpc.show_marker_at_current_position()
def _update_widgets_based_on_table_state(self):
index, eline = self._get_current_index_in_table()
if index >= 0:
# Selection exists. Update the state of element selection widget.
self.element_selection.set_current_item(eline)
else:
# No selection, update the state based on element selection widget.
eline = self._selected_eline
self.tbl_elines_set_selection(eline)
self._update_add_remove_btn_state(eline)
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def _update_eline_selection_list(self):
self._eline_list = self.gpc.get_full_eline_list()
self.element_selection.set_item_list(self._eline_list)
self.signal_update_element_selection_list.emit()
@Slot()
def update_eline_table(self):
"""Update table of emission lines without changing anything else"""
eline_table = self.gpc.get_selected_eline_table()
self.fill_eline_table(eline_table)
def _get_eline_index_in_table(self, eline):
try:
index = [_["eline"] for _ in self._table_contents].index(eline)
except ValueError:
index = -1
return index
def _get_eline_index_in_list(self, eline):
try:
index = self._eline_list.index(eline)
except ValueError:
index = -1
return index
def _get_current_index_in_table(self):
sel_ranges = self.tbl_elines.selectedRanges()
# The table is configured to have one or no selected ranges
# 'Open' button should be enabled only if a range (row) is selected
if sel_ranges:
index = sel_ranges[0].topRow()
eline = self._table_contents[index]["eline"]
else:
index, eline = -1, ""
return index, eline
def _get_current_index_in_list(self):
index, eline = self.element_selection.get_current_item()
return index, eline
def _update_add_remove_btn_state(self, eline=None):
if eline is None:
index_in_table, eline = self._get_current_index_in_table()
index_in_list, eline = self._get_current_index_in_list()
else:
index_in_table = self._get_eline_index_in_table(eline)
index_in_list = self._get_eline_index_in_list(eline)
add_enabled, remove_enabled = True, True
if index_in_list < 0 and index_in_table < 0:
add_enabled, remove_enabled = False, False
else:
if index_in_table >= 0:
if self.gpc.get_eline_name_category(eline) != "other":
add_enabled = False
else:
add_enabled, remove_enabled = False, False
else:
remove_enabled = False
self.pb_add_eline.setEnabled(add_enabled)
self.pb_remove_eline.setEnabled(remove_enabled)
self.signal_update_add_remove_btn_state.emit(add_enabled,
remove_enabled)
def _update_add_edit_userpeak_btn_state(self):
enabled = True
add_peak = True
if self.gpc.get_eline_name_category(
self._selected_eline) == "userpeak":
add_peak = False
# Finally check if marker is set (you need it for adding peaks)
_, marker_set = self.gpc.get_suggested_manual_peak_energy()
if not marker_set and add_peak:
enabled = False
if add_peak:
btn_text = "New User Peak ..."
else:
btn_text = "Edit User Peak ..."
self.pb_user_peaks.setText(btn_text)
self.pb_user_peaks.setEnabled(enabled)
def _update_add_edit_pileup_peak_btn_state(self):
enabled = True
if self.gpc.get_eline_name_category(self._selected_eline) == "pileup":
enabled = False
# Finally check if marker is set (you need it for adding peaks)
_, marker_set = self.gpc.get_suggested_manual_peak_energy()
# Ignore set marker for userpeaks (marker is used to display location of userpeaks)
if self.gpc.get_eline_name_category(
self._selected_eline) == "userpeak":
marker_set = False
if not marker_set:
enabled = False
self.pb_pileup_peaks.setEnabled(enabled)
def _set_selected_eline(self, eline):
self._update_add_remove_btn_state(eline)
if eline != self._selected_eline:
self._selected_eline = eline
self.gpc.set_selected_eline(eline)
self._display_peak_intensity(eline)
else:
# Peak intensity may change in some circumstances, so renew the displayed value.
self._display_peak_intensity(eline)
# Update button states after 'self._selected_eline' is set
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def _set_fit_status(self, status):
self.gui_vars["gui_state"]["state_model_fit_exists"] = status
self.signal_parameters_changed.emit()
class ReactionMask(QWidget):
"""The input mask for a reaction"""
def __init__(self, parent: ReactionList):
QWidget.__init__(self)
self.parent = parent
self.reaction = None
self.is_valid = True
self.changed = False
self.setAcceptDrops(False)
layout = QVBoxLayout()
l = QHBoxLayout()
self.delete_button = QPushButton("Delete reaction")
self.delete_button.setIcon(QIcon.fromTheme("edit-delete"))
policy = QSizePolicy()
policy.ShrinkFlag = True
self.delete_button.setSizePolicy(policy)
l.addWidget(self.delete_button)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Id:")
self.id = QLineEdit()
l.addWidget(label)
l.addWidget(self.id)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Name:")
self.name = QLineEdit()
l.addWidget(label)
l.addWidget(self.name)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Equation:")
self.equation = QLineEdit()
l.addWidget(label)
l.addWidget(self.equation)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Rate min:")
self.lower_bound = QLineEdit()
l.addWidget(label)
l.addWidget(self.lower_bound)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Rate max:")
self.upper_bound = QLineEdit()
l.addWidget(label)
l.addWidget(self.upper_bound)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Coefficient in obj. function:")
self.coefficent = QLineEdit()
l.addWidget(label)
l.addWidget(self.coefficent)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Gene reaction rule:")
self.gene_reaction_rule = QLineEdit()
l.addWidget(label)
l.addWidget(self.gene_reaction_rule)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Annotations:")
l.addWidget(label)
l2 = QHBoxLayout()
self.annotation = QTableWidget(0, 2)
self.annotation.setHorizontalHeaderLabels(
["key", "value"])
self.annotation.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
l2.addWidget(self.annotation)
self.add_anno = QPushButton("+")
self.add_anno.clicked.connect(self.add_anno_row)
l2.addWidget(self.add_anno)
l.addItem(l2)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Metabolites involved in this reaction:")
l.addWidget(label)
l2 = QHBoxLayout()
self.metabolites = QTreeWidget()
self.metabolites.setHeaderLabels(["Id"])
self.metabolites.setSortingEnabled(True)
l2.addWidget(self.metabolites)
l.addItem(l2)
self.metabolites.itemDoubleClicked.connect(
self.emit_jump_to_metabolite)
layout.addItem(l)
self.jump_list = JumpList(self)
layout.addWidget(self.jump_list)
self.setLayout(layout)
self.delete_button.clicked.connect(self.delete_reaction)
self.throttler = SignalThrottler(500)
self.throttler.triggered.connect(self.reaction_data_changed)
self.id.textEdited.connect(self.throttler.throttle)
self.name.textEdited.connect(self.throttler.throttle)
self.equation.textEdited.connect(self.throttler.throttle)
self.lower_bound.textEdited.connect(self.throttler.throttle)
self.upper_bound.textEdited.connect(self.throttler.throttle)
self.coefficent.textEdited.connect(self.throttler.throttle)
self.gene_reaction_rule.textEdited.connect(self.throttler.throttle)
self.annotation.itemChanged.connect(self.throttler.throttle)
self.validate_mask()
def add_anno_row(self):
i = self.annotation.rowCount()
self.annotation.insertRow(i)
self.changed = True
def apply(self):
try:
self.reaction.id = self.id.text()
except ValueError:
turn_red(self.id)
QMessageBox.information(
self, 'Invalid id', 'Could not apply changes identifier ' +
self.id.text() + ' already used.')
else:
self.reaction.name = self.name.text()
self.reaction.build_reaction_from_string(self.equation.text())
self.reaction.lower_bound = float(self.lower_bound.text())
self.reaction.upper_bound = float(self.upper_bound.text())
self.reaction.objective_coefficient = float(self.coefficent.text())
self.reaction.gene_reaction_rule = self.gene_reaction_rule.text()
self.reaction.annotation = {}
rows = self.annotation.rowCount()
for i in range(0, rows):
key = self.annotation.item(i, 0).text()
if self.annotation.item(i, 1) is None:
value = ""
else:
value = self.annotation.item(i, 1).text()
self.reaction.annotation[key] = value
self.changed = False
self.reactionChanged.emit(self.reaction)
def delete_reaction(self):
self.hide()
self.reactionDeleted.emit(self.reaction)
def validate_id(self):
with self.parent.appdata.project.cobra_py_model as model:
try:
r = cobra.Reaction(id=self.id.text())
model.add_reaction(r)
except ValueError:
turn_red(self.id)
return False
else:
turn_white(self.id)
return True
def validate_name(self):
with self.parent.appdata.project.cobra_py_model as model:
try:
r = cobra.Reaction(id="testid", name=self.name.text())
model.add_reaction(r)
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_equation(self):
ok = False
test_reaction = cobra.Reaction(
"xxxx_cnapy_test_reaction", name="cnapy test reaction")
with self.parent.appdata.project.cobra_py_model as model:
model.add_reaction(test_reaction)
try:
eqtxt = self.equation.text().rstrip()
if len(eqtxt) > 0 and eqtxt[-1] == '+':
turn_red(self.equation)
else:
test_reaction.build_reaction_from_string(eqtxt)
turn_white(self.equation)
ok = True
except ValueError:
turn_red(self.equation)
try:
test_reaction = self.parent.appdata.project.cobra_py_model.reactions.get_by_id(
"xxxx_cnapy_test_reaction")
self.parent.appdata.project.cobra_py_model.remove_reactions(
[test_reaction], remove_orphans=True)
except KeyError:
pass
return ok
def validate_lowerbound(self):
try:
_x = float(self.lower_bound.text())
except ValueError:
turn_red(self.lower_bound)
return False
else:
turn_white(self.lower_bound)
return True
def validate_upperbound(self):
try:
_x = float(self.upper_bound.text())
except ValueError:
turn_red(self.upper_bound)
return False
else:
turn_white(self.upper_bound)
return True
def validate_coefficient(self):
try:
_x = float(self.coefficent.text())
except ValueError:
turn_red(self.coefficent)
return False
else:
turn_white(self.coefficent)
return True
def validate_gene_reaction_rule(self):
try:
_x = float(self.gene_reaction_rule.text())
except ValueError:
turn_red(self.gene_reaction_rule)
return False
else:
turn_white(self.gene_reaction_rule)
return True
def validate_mask(self):
valid_id = self.validate_id()
valid_name = self.validate_name()
valid_equation = self.validate_equation()
valid_lb = self.validate_lowerbound()
valid_ub = self.validate_upperbound()
valid_coefficient = self.validate_coefficient()
if valid_id & valid_name & valid_equation & valid_lb & valid_ub & valid_coefficient:
self.is_valid = True
else:
self.is_valid = False
def reaction_data_changed(self):
self.changed = True
self.validate_mask()
if self.is_valid:
self.apply()
self.update_state()
def update_state(self):
self.jump_list.clear()
for name, m in self.parent.appdata.project.maps.items():
if self.id.text() in m["boxes"]:
self.jump_list.add(name)
self.metabolites.clear()
if self.parent.appdata.project.cobra_py_model.reactions.has_id(self.id.text()):
reaction = self.parent.appdata.project.cobra_py_model.reactions.get_by_id(
self.id.text())
for m in reaction.metabolites:
item = QTreeWidgetItem(self.metabolites)
item.setText(0, m.id)
item.setText(1, m.name)
item.setData(2, 0, m)
text = "Id: " + m.id + "\nName: " + m.name
item.setToolTip(1, text)
def emit_jump_to_map(self, name):
self.jumpToMap.emit(name, self.id.text())
def emit_jump_to_metabolite(self, metabolite):
self.jumpToMetabolite.emit(str(metabolite.data(2, 0)))
jumpToMap = Signal(str, str)
jumpToMetabolite = Signal(str)
reactionChanged = Signal(cobra.Reaction)
reactionDeleted = Signal(cobra.Reaction)
class MeasurementWidget(QWidget):
"""
:type settings: Settings
:type segment: Segment
"""
def __init__(self, settings: PartSettings, segment=None):
super().__init__()
self.settings = settings
self.segment = segment
self.measurements_storage = MeasurementsStorage()
self.recalculate_button = QPushButton(
"Recalculate and\n replace measurement", self)
self.recalculate_button.clicked.connect(
self.replace_measurement_result)
self.recalculate_append_button = QPushButton(
"Recalculate and\n append measurement", self)
self.recalculate_append_button.clicked.connect(
self.append_measurement_result)
self.copy_button = QPushButton("Copy to clipboard", self)
self.copy_button.setToolTip(
"You cacn copy also with 'Ctrl+C'. To get raw copy copy with 'Ctrl+Shit+C'"
)
self.horizontal_measurement_present = QCheckBox(
"Horizontal view", self)
self.no_header = QCheckBox("No header", self)
self.no_units = QCheckBox("No units", self)
self.no_units.setChecked(True)
self.no_units.clicked.connect(self.refresh_view)
self.expand_mode = QCheckBox("Expand", self)
self.expand_mode.setToolTip(
"Shows results for each component in separate entry")
self.file_names = EnumComboBox(FileNamesEnum)
self.file_names_label = QLabel("Add file name:")
self.file_names.currentIndexChanged.connect(self.refresh_view)
self.horizontal_measurement_present.stateChanged.connect(
self.refresh_view)
self.expand_mode.stateChanged.connect(self.refresh_view)
self.copy_button.clicked.connect(self.copy_to_clipboard)
self.measurement_type = SearchCombBox(self)
# noinspection PyUnresolvedReferences
self.measurement_type.currentIndexChanged.connect(
self.measurement_profile_selection_changed)
self.measurement_type.addItem("<none>")
self.measurement_type.addItems(
list(sorted(self.settings.measurement_profiles.keys())))
self.measurement_type.setToolTip(
'You can create new measurement profile in advanced window, in tab "Measurement settings"'
)
self.channels_chose = ChannelComboBox()
self.units_choose = EnumComboBox(Units)
self.units_choose.set_value(self.settings.get("units_value", Units.nm))
self.info_field = QTableWidget(self)
self.info_field.setColumnCount(3)
self.info_field.setHorizontalHeaderLabels(["Name", "Value", "Units"])
self.measurement_add_shift = 0
layout = QVBoxLayout()
# layout.addWidget(self.recalculate_button)
v_butt_layout = QVBoxLayout()
v_butt_layout.setSpacing(1)
self.up_butt_layout = QHBoxLayout()
self.up_butt_layout.addWidget(self.recalculate_button)
self.up_butt_layout.addWidget(self.recalculate_append_button)
self.butt_layout = QHBoxLayout()
# self.butt_layout.setMargin(0)
# self.butt_layout.setSpacing(10)
self.butt_layout.addWidget(self.horizontal_measurement_present, 1)
self.butt_layout.addWidget(self.no_header, 1)
self.butt_layout.addWidget(self.no_units, 1)
self.butt_layout.addWidget(self.expand_mode, 1)
self.butt_layout.addWidget(self.file_names_label)
self.butt_layout.addWidget(self.file_names, 1)
self.butt_layout.addWidget(self.copy_button, 2)
self.butt_layout2 = QHBoxLayout()
self.butt_layout3 = QHBoxLayout()
self.butt_layout3.addWidget(QLabel("Channel:"))
self.butt_layout3.addWidget(self.channels_chose)
self.butt_layout3.addWidget(QLabel("Units:"))
self.butt_layout3.addWidget(self.units_choose)
# self.butt_layout3.addWidget(QLabel("Noise removal:"))
# self.butt_layout3.addWidget(self.noise_removal_method)
self.butt_layout3.addWidget(QLabel("Measurement set:"))
self.butt_layout3.addWidget(self.measurement_type, 2)
v_butt_layout.addLayout(self.up_butt_layout)
v_butt_layout.addLayout(self.butt_layout)
v_butt_layout.addLayout(self.butt_layout2)
v_butt_layout.addLayout(self.butt_layout3)
layout.addLayout(v_butt_layout)
# layout.addLayout(self.butt_layout)
layout.addWidget(self.info_field)
self.setLayout(layout)
# noinspection PyArgumentList
self.clip = QApplication.clipboard()
self.settings.image_changed[int].connect(self.image_changed)
self.previous_profile = None
def check_if_measurement_can_be_calculated(self, name):
if name == "<none>":
return "<none>"
profile: MeasurementProfile = self.settings.measurement_profiles.get(
name)
if profile.is_any_mask_measurement() and self.settings.mask is None:
QMessageBox.information(
self, "Need mask",
"To use this measurement set please use data with mask loaded",
QMessageBox.Ok)
self.measurement_type.setCurrentIndex(0)
return "<none>"
if self.settings.roi is None:
QMessageBox.information(
self,
"Need segmentation",
'Before calculating please create segmentation ("Execute" button)',
QMessageBox.Ok,
)
self.measurement_type.setCurrentIndex(0)
return "<none>"
return name
def image_changed(self, channels_num):
self.channels_chose.change_channels_num(channels_num)
def measurement_profile_selection_changed(self, index):
text = self.measurement_type.itemText(index)
text = self.check_if_measurement_can_be_calculated(text)
try:
stat = self.settings.measurement_profiles[text]
is_mask = stat.is_any_mask_measurement()
disable = is_mask and (self.settings.mask is None)
except KeyError:
disable = True
self.recalculate_button.setDisabled(disable)
self.recalculate_append_button.setDisabled(disable)
if disable:
self.recalculate_button.setToolTip(
"Measurement profile contains mask measurements when mask is not loaded"
)
self.recalculate_append_button.setToolTip(
"Measurement profile contains mask measurements when mask is not loaded"
)
else:
self.recalculate_button.setToolTip("")
self.recalculate_append_button.setToolTip("")
def copy_to_clipboard(self):
s = ""
for r in range(self.info_field.rowCount()):
for c in range(self.info_field.columnCount()):
try:
s += str(self.info_field.item(r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" # eliminate last '\t'
self.clip.setText(s)
def replace_measurement_result(self):
self.measurements_storage.clear()
self.previous_profile = ""
self.append_measurement_result()
def refresh_view(self):
self.measurements_storage.set_expand(self.expand_mode.isChecked())
self.measurements_storage.set_show_units(not self.no_units.isChecked())
self.info_field.clear()
save_orientation = self.horizontal_measurement_present.isChecked()
columns, rows = self.measurements_storage.get_size(save_orientation)
self.info_field.setColumnCount(columns)
self.info_field.setRowCount(rows)
self.info_field.setHorizontalHeaderLabels(
self.measurements_storage.get_header(save_orientation))
self.info_field.setVerticalHeaderLabels(
self.measurements_storage.get_rows(save_orientation))
for x in range(rows):
for y in range(columns):
self.info_field.setItem(
x, y,
QTableWidgetItem(
self.measurements_storage.get_val_as_str(
x, y, save_orientation)))
if self.file_names.get_value() == FileNamesEnum.No:
if save_orientation:
self.info_field.removeColumn(0)
else:
self.info_field.removeRow(0)
elif self.file_names.get_value() == FileNamesEnum.Short:
if save_orientation:
columns = 1
else:
rows = 1
for x in range(rows):
for y in range(columns):
item = self.info_field.item(x, y)
item.setText(os.path.basename(item.text()))
self.info_field.setEditTriggers(QAbstractItemView.NoEditTriggers)
def append_measurement_result(self):
try:
compute_class = self.settings.measurement_profiles[
self.measurement_type.currentText()]
except KeyError:
QMessageBox.warning(
self,
"Measurement profile not found",
f"Measurement profile '{self.measurement_type.currentText()}' not found'",
)
return
if self.settings.roi is None:
return
units = self.units_choose.get_value()
# FIXME find which errors should be displayed as warning
# def exception_hook(exception):
# QMessageBox.warning(self, "Calculation error", f"Error during calculation: {exception}")
for num in compute_class.get_channels_num():
if num >= self.settings.image.channels:
QMessageBox.warning(
self,
"Measurement error",
"Cannot calculate this measurement because "
f"image do not have channel {num+1}",
)
return
thread = ExecuteFunctionThread(
compute_class.calculate,
[
self.settings.image,
self.channels_chose.currentIndex(), self.settings.roi_info,
units
],
)
dial = WaitingDialog(
thread,
"Measurement calculation") # , exception_hook=exception_hook)
dial.exec()
stat: MeasurementResult = thread.result
if stat is None:
return
stat.set_filename(self.settings.image_path)
self.measurements_storage.add_measurements(stat)
self.previous_profile = compute_class.name
self.refresh_view()
def keyPressEvent(self, e: QKeyEvent):
if e.modifiers() & Qt.ControlModifier:
selected = self.info_field.selectedRanges()
if e.key() == Qt.Key_C: # copy
s = ""
for r in range(selected[0].topRow(),
selected[0].bottomRow() + 1):
for c in range(selected[0].leftColumn(),
selected[0].rightColumn() + 1):
try:
s += str(self.info_field.item(r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" # eliminate last '\t'
self.clip.setText(s)
def update_measurement_list(self):
self.measurement_type.blockSignals(True)
available = list(sorted(self.settings.measurement_profiles.keys()))
text = self.measurement_type.currentText()
try:
index = available.index(text) + 1
except ValueError:
index = 0
self.measurement_type.clear()
self.measurement_type.addItem("<none>")
self.measurement_type.addItems(available)
self.measurement_type.setCurrentIndex(index)
self.measurement_type.blockSignals(False)
def showEvent(self, _):
self.update_measurement_list()
def event(self, event: QEvent):
if event.type() == QEvent.WindowActivate:
self.update_measurement_list()
return super().event(event)
@staticmethod
def _move_widgets(widgets_list: List[Tuple[QWidget, int]],
layout1: QBoxLayout, layout2: QBoxLayout):
for el in widgets_list:
layout1.removeWidget(el[0])
layout2.addWidget(el[0], el[1])
def resizeEvent(self, _event: QResizeEvent) -> None:
if self.width() < 800 and self.butt_layout2.count() == 0:
self._move_widgets(
[(self.file_names_label, 1), (self.file_names, 1),
(self.copy_button, 2)],
self.butt_layout,
self.butt_layout2,
)
elif self.width() > 800 and self.butt_layout2.count() != 0:
self._move_widgets(
[(self.file_names_label, 1), (self.file_names, 1),
(self.copy_button, 2)],
self.butt_layout2,
self.butt_layout,
)
class MetabolitesMask(QWidget):
"""The input mask for a metabolites"""
def __init__(self, appdata):
QWidget.__init__(self)
self.appdata = appdata
self.metabolite = None
self.is_valid = True
self.changed = False
self.setAcceptDrops(False)
layout = QVBoxLayout()
l = QHBoxLayout()
label = QLabel("Id:")
self.id = QLineEdit()
l.addWidget(label)
l.addWidget(self.id)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Name:")
self.name = QLineEdit()
l.addWidget(label)
l.addWidget(self.name)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Formula:")
self.formula = QLineEdit()
l.addWidget(label)
l.addWidget(self.formula)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Charge:")
self.charge = QLineEdit()
l.addWidget(label)
l.addWidget(self.charge)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Compartment:")
self.compartment = QLineEdit()
l.addWidget(label)
l.addWidget(self.compartment)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Annotations:")
l.addWidget(label)
l2 = QHBoxLayout()
self.annotation = QTableWidget(0, 2)
self.annotation.setHorizontalHeaderLabels(
["key", "value"])
self.annotation.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
l2.addWidget(self.annotation)
self.add_anno = QPushButton("+")
self.add_anno.clicked.connect(self.add_anno_row)
l2.addWidget(self.add_anno)
l.addItem(l2)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Reactions using this metabolite:")
l.addWidget(label)
l2 = QHBoxLayout()
self.reactions = QTreeWidget()
self.reactions.setHeaderLabels(["Id"])
self.reactions.setSortingEnabled(True)
l2.addWidget(self.reactions)
l.addItem(l2)
self.reactions.itemDoubleClicked.connect(self.emit_jump_to_reaction)
layout.addItem(l)
self.setLayout(layout)
self.throttler = SignalThrottler(500)
self.throttler.triggered.connect(self.metabolites_data_changed)
self.id.textEdited.connect(self.throttler.throttle)
self.name.textEdited.connect(self.throttler.throttle)
self.formula.textEdited.connect(self.throttler.throttle)
self.charge.textEdited.connect(self.throttler.throttle)
self.compartment.textEdited.connect(self.throttler.throttle)
self.annotation.itemChanged.connect(self.throttler.throttle)
self.validate_mask()
def add_anno_row(self):
i = self.annotation.rowCount()
self.annotation.insertRow(i)
self.changed = True
def apply(self):
try:
self.metabolite.id = self.id.text()
except ValueError:
turn_red(self.id)
QMessageBox.information(
self, 'Invalid id', 'Could not apply changes identifier ' +
self.id.text()+' already used.')
else:
self.metabolite.name = self.name.text()
self.metabolite.formula = self.formula.text()
if self.charge.text() == "":
self.metabolite.charge = None
else:
self.metabolite.charge = int(self.charge.text())
self.metabolite.compartment = self.compartment.text()
self.metabolite.annotation = {}
rows = self.annotation.rowCount()
for i in range(0, rows):
key = self.annotation.item(i, 0).text()
if self.annotation.item(i, 1) is None:
value = ""
else:
value = self.annotation.item(i, 1).text()
self.metabolite.annotation[key] = value
self.changed = False
self.metaboliteChanged.emit(self.metabolite)
def validate_id(self):
with self.appdata.project.cobra_py_model as model:
text = self.id.text()
if text == "":
turn_red(self.id)
return False
if ' ' in text:
turn_red(self.id)
return False
try:
m = cobra.Metabolite(id=self.id.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.id)
return False
else:
turn_white(self.id)
return True
def validate_name(self):
with self.appdata.project.cobra_py_model as model:
try:
m = cobra.Metabolite(id="test_id", name=self.name.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_formula(self):
return True
def validate_charge(self):
try:
if self.charge.text() != "":
_x = int(self.charge.text())
except ValueError:
turn_red(self.charge)
return False
else:
turn_white(self.charge)
return True
def validate_compartment(self):
try:
if ' ' in self.compartment.text():
turn_red(self.compartment)
return False
if '-' in self.compartment.text():
turn_red(self.compartment)
return False
_m = cobra.Metabolite(id="test_id", name=self.compartment.text())
except ValueError:
turn_red(self.compartment)
return False
else:
turn_white(self.compartment)
return True
def validate_mask(self):
valid_id = self.validate_id()
valid_name = self.validate_name()
valid_formula = self.validate_formula()
valid_charge = self.validate_charge()
valid_compartment = self.validate_compartment()
if valid_id & valid_name & valid_formula & valid_charge & valid_compartment:
self.is_valid = True
else:
self.is_valid = False
def metabolites_data_changed(self):
self.changed = True
self.validate_mask()
if self.is_valid:
self.apply()
self.update_state()
def update_state(self):
self.reactions.clear()
if self.appdata.project.cobra_py_model.metabolites.has_id(self.id.text()):
metabolite = self.appdata.project.cobra_py_model.metabolites.get_by_id(
self.id.text())
for r in metabolite.reactions:
item = QTreeWidgetItem(self.reactions)
item.setText(0, r.id)
item.setText(1, r.name)
item.setData(2, 0, r)
text = "Id: " + r.id + "\nName: " + r.name
item.setToolTip(1, text)
def emit_jump_to_reaction(self, reaction):
self.jumpToReaction.emit(reaction.data(2, 0).id)
jumpToReaction = Signal(str)
metaboliteChanged = Signal(cobra.Metabolite)
class RgbSelectionWidget(QWidget):
signal_update_map_selections = Signal()
def __init__(self):
super().__init__()
self._range_table = []
self._limit_table = []
self._rgb_keys = ["red", "green", "blue"]
self._rgb_dict = {_: None for _ in self._rgb_keys}
widget_layout = self._setup_rgb_widget()
self.setLayout(widget_layout)
sp = QSizePolicy()
sp.setControlType(QSizePolicy.PushButton)
sp.setHorizontalPolicy(QSizePolicy.Expanding)
sp.setVerticalPolicy(QSizePolicy.Fixed)
self.setSizePolicy(sp)
def _setup_rgb_element(self, n_row, *, rb_check=0):
"""
Parameters
----------
rb_check: int
The number of QRadioButton to check. Typically this would be the row number.
"""
combo_elements = ComboBoxNamed(name=f"{n_row}")
# combo_elements.setSizeAdjustPolicy(QComboBox.AdjustToContents)
# Set text color for QComboBox widget (necessary if the program is used with Dark theme)
pal = combo_elements.palette()
pal.setColor(QPalette.ButtonText, Qt.black)
combo_elements.setPalette(pal)
# Set text color for drop-down view (necessary if the program is used with Dark theme)
pal = combo_elements.view().palette()
pal.setColor(QPalette.Text, Qt.black)
combo_elements.view().setPalette(pal)
btns = [QRadioButton(), QRadioButton(), QRadioButton()]
if 0 <= rb_check < len(btns):
btns[rb_check].setChecked(True)
# Color is set for operation with Dark theme
for btn in btns:
pal = btn.palette()
pal.setColor(QPalette.Text, Qt.black)
btn.setPalette(pal)
btn_group = QButtonGroup()
for btn in btns:
btn_group.addButton(btn)
rng = RangeManager(name=f"{n_row}", add_sliders=True)
rng.setTextColor([0, 0, 0]) # Set text color to 'black'
# Set some text in edit boxes (just to demonstrate how the controls will look like)
rng.le_min_value.setText("0.0")
rng.le_max_value.setText("1.0")
rng.setAlignment(Qt.AlignCenter)
return combo_elements, btns, rng, btn_group
def _enable_selection_events(self, enable):
if enable:
if not self.elements_btn_groups_events_enabled:
for btn_group in self.elements_btn_groups:
btn_group.buttonToggled.connect(self.rb_toggled)
for el_combo in self.elements_combo:
el_combo.currentIndexChanged.connect(
self.combo_element_current_index_changed)
for el_range in self.elements_range:
el_range.selection_changed.connect(
self.range_selection_changed)
self.elements_btn_groups_events_enabled = True
else:
if self.elements_btn_groups_events_enabled:
for btn_group in self.elements_btn_groups:
btn_group.buttonToggled.disconnect(self.rb_toggled)
for el_combo in self.elements_combo:
el_combo.currentIndexChanged.disconnect(
self.combo_element_current_index_changed)
# Disconnecting the Range Manager signals is not necessary, but let's do it for consistency
for el_range in self.elements_range:
el_range.selection_changed.disconnect(
self.range_selection_changed)
self.elements_btn_groups_events_enabled = False
def _setup_rgb_widget(self):
self.elements_combo = []
self.elements_rb_color = []
self.elements_range = []
self.elements_btn_groups = []
self.elements_btn_groups_events_enabled = False
self.row_colors = []
self.table = QTableWidget()
# Horizontal header entries
tbl_labels = ["Element", "Red", "Green", "Blue", "Range"]
# The list of columns that stretch with the table
self.tbl_cols_stretch = ("Range", )
self.table.setColumnCount(len(tbl_labels))
self.table.setRowCount(3)
self.table.setHorizontalHeaderLabels(tbl_labels)
self.table.verticalHeader().hide()
self.table.setSelectionMode(QTableWidget.NoSelection)
header = self.table.horizontalHeader()
for n, lbl in enumerate(tbl_labels):
# Set stretching for the columns
if lbl in self.tbl_cols_stretch:
header.setSectionResizeMode(n, QHeaderView.Stretch)
else:
header.setSectionResizeMode(n, QHeaderView.ResizeToContents)
vheader = self.table.verticalHeader()
vheader.setSectionResizeMode(QHeaderView.Stretch) # ResizeToContents)
for n_row in range(3):
combo_elements, btns, rng, btn_group = self._setup_rgb_element(
n_row, rb_check=n_row)
combo_elements.setMinimumWidth(180)
self.table.setCellWidget(n_row, 0, combo_elements)
for i, btn in enumerate(btns):
item = QWidget()
item_hbox = QHBoxLayout(item)
item_hbox.addWidget(btn)
item_hbox.setAlignment(Qt.AlignCenter)
item_hbox.setContentsMargins(0, 0, 0, 0)
item.setMinimumWidth(70)
self.table.setCellWidget(n_row, i + 1, item)
rng.setMinimumWidth(200)
rng.setMaximumWidth(400)
self.table.setCellWidget(n_row, 4, rng)
self.elements_combo.append(combo_elements)
self.elements_rb_color.append(btns)
self.elements_range.append(rng)
self.elements_btn_groups.append(btn_group)
self.row_colors.append(self._rgb_keys[n_row])
# Colors that are used to paint rows of the table in RGB colors
br = 150
self._rgb_row_colors = {
"red": (255, br, br),
"green": (br, 255, br),
"blue": (br, br, 255)
}
self._rgb_color_keys = ["red", "green", "blue"]
# Set initial colors
for n_row in range(self.table.rowCount()):
self._set_row_color(n_row)
self._enable_selection_events(True)
self.table.resizeRowsToContents()
# Table height is computed based on content. It doesn't seem
# to account for the height of custom widgets, but the table
# looks good enough
table_height = 0
for n_row in range(self.table.rowCount()):
table_height += self.table.rowHeight(n_row)
self.table.setMaximumHeight(table_height)
table_width = 650
self.table.setMinimumWidth(table_width)
self.table.setMaximumWidth(800)
hbox = QHBoxLayout()
hbox.addWidget(self.table)
return hbox
def combo_element_current_index_changed(self, name, index):
if index < 0 or index >= len(self._range_table):
return
n_row = int(name)
sel_eline = self._range_table[index][0]
row_color = self.row_colors[n_row]
self._rgb_dict[row_color] = sel_eline
self.elements_range[n_row].set_range(self._range_table[index][1],
self._range_table[index][2])
self.elements_range[n_row].set_selection(
value_low=self._limit_table[index][1],
value_high=self._limit_table[index][2])
self._update_map_selections()
def range_selection_changed(self, v_low, v_high, name):
n_row = int(name)
row_color = self.row_colors[n_row]
sel_eline = self._rgb_dict[row_color]
ind = None
try:
ind = [_[0] for _ in self._limit_table].index(sel_eline)
except ValueError:
pass
if ind is not None:
self._limit_table[ind][1] = v_low
self._limit_table[ind][2] = v_high
self._update_map_selections()
# We are not preventing users to select the same emission line in to rows.
# Update the selected limits in other rows where the same element is selected.
for nr, el_range in enumerate(self.elements_range):
if (nr != n_row) and (self._rgb_dict[self.row_colors[nr]]
== sel_eline):
el_range.set_selection(value_low=v_low, value_high=v_high)
def _get_selected_row_color(self, n_row):
color_key = None
btns = self.elements_rb_color[n_row]
for n, btn in enumerate(btns):
if btn.isChecked():
color_key = self._rgb_color_keys[n]
break
return color_key
def _set_row_color(self, n_row, *, color_key=None):
"""
Parameters
----------
n_row: int
The row number that needs background color change (0..2 if table has 3 rows)
color_key: int
Color key: "red", "green" or "blue"
"""
if color_key is None:
color_key = self._get_selected_row_color(n_row)
if color_key is None:
return
self.row_colors[n_row] = color_key
rgb = self._rgb_row_colors[color_key]
# The following code is based on the arrangement of the widgets in the table
# Modify the code if widgets are arranged differently or the table structure
# is changed
for n_col in range(self.table.columnCount()):
wd = self.table.cellWidget(n_row, n_col)
if n_col == 0:
# Combo box: update both QComboBox and QWidget backgrounds
# QWidget - background of the drop-down selection list
css1 = get_background_css(rgb,
widget="QComboBox",
editable=False)
css2 = get_background_css(rgb, widget="QWidget", editable=True)
wd.setStyleSheet(css2 + css1)
elif n_col <= 3:
# 3 QRadioButton's. The buttons are inserted into QWidget objects,
# and we need to change backgrounds of QWidgets, not only buttons.
wd.setStyleSheet(
get_background_css(rgb, widget="QWidget", editable=False))
elif n_col == 4:
# Custom RangeManager widget, color is updated using custom method
wd.setBackground(rgb)
n_col = self._rgb_color_keys.index(color_key)
for n, n_btn in enumerate(self.elements_rb_color[n_row]):
check_status = True if n == n_col else False
n_btn.setChecked(check_status)
def _fill_table(self):
self._enable_selection_events(False)
eline_list = [_[0] for _ in self._range_table]
for n_row in range(self.table.rowCount()):
self.elements_combo[n_row].clear()
self.elements_combo[n_row].addItems(eline_list)
for n_row, color in enumerate(self._rgb_color_keys):
# Initially set colors in order
self._set_row_color(n_row, color_key=color)
eline_key = self._rgb_dict[color]
if eline_key is not None:
try:
ind = eline_list.index(eline_key)
self.elements_combo[n_row].setCurrentIndex(ind)
range_low, range_high = self._range_table[ind][1:]
self.elements_range[n_row].set_range(range_low, range_high)
sel_low, sel_high = self._limit_table[ind][1:]
self.elements_range[n_row].set_selection(
value_low=sel_low, value_high=sel_high)
except ValueError:
pass
else:
self.elements_combo[n_row].setCurrentIndex(-1) # Deselect all
self.elements_range[n_row].set_range(0, 1)
self.elements_range[n_row].set_selection(value_low=0,
value_high=1)
self._enable_selection_events(True)
def _find_rbutton(self, button):
for nr, btns in enumerate(self.elements_rb_color):
for nc, btn in enumerate(btns):
if btn == button:
# Return tuple (nr, nc)
return nr, nc
# Return None if the button is not found (this shouldn't happen)
return None
def rb_toggled(self, button, state):
if state: # Ignore signals from unchecked buttons
nr, nc = self._find_rbutton(button)
color_current = self.row_colors[nr]
color_to_set = self._rgb_color_keys[nc]
nr_switch = self.row_colors.index(color_to_set)
self._enable_selection_events(False)
self._set_row_color(nr, color_key=color_to_set)
self._set_row_color(nr_switch, color_key=color_current)
# Swap selected maps
tmp = self._rgb_dict[color_to_set]
self._rgb_dict[color_to_set] = self._rgb_dict[color_current]
self._rgb_dict[color_current] = tmp
self._enable_selection_events(True)
self._update_map_selections()
def set_ranges_and_limits(self,
*,
range_table=None,
limit_table=None,
rgb_dict=None):
if range_table is not None:
self._range_table = copy.deepcopy(range_table)
if limit_table is not None:
self._limit_table = copy.deepcopy(limit_table)
if rgb_dict is not None:
self._rgb_dict = rgb_dict.copy()
self._fill_table()
def _update_map_selections(self):
"""Upload the selections (limit table) and update plot"""
self.signal_update_map_selections.emit()
class PMGRuleCtrl(BaseExtendedWidget):
"""
rules:
{'name':'regex',
'text':'匹配正则表达式',
'init':False
}
"""
def __init__(self,
layout_dir='v',
title='',
rules: List[Dict[str, Union[bool, int, float, str]]] = None):
super().__init__(layout_dir)
self.table_h_headers = []
self.table_keys = []
self.initial_values = []
for rule in rules:
self.table_h_headers.append(rule['text'])
self.table_keys.append(rule['name'])
self.initial_values.append(rule['init'])
self.regulations_table = QTableWidget(0, len(self.table_h_headers))
self.regulations_table.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.regulations_table.setHorizontalHeaderLabels(self.table_h_headers)
self.layout().addWidget(self.regulations_table)
self.set_layout = QHBoxLayout()
self.layout().addLayout(self.set_layout)
self.button_add = QPushButton('Add')
self.button_remove = QPushButton('Remove')
self.set_layout.addWidget(self.button_add)
self.set_layout.addWidget(self.button_remove)
self.button_add.clicked.connect(self.add_regulation)
self.button_remove.clicked.connect(self.remove_regulation)
def load_regulations(self, regulations: List[Dict[str,
Union[int, str, float,
bool]]]):
row_count = len(regulations)
self.regulations_table.setRowCount(row_count)
for i, regulation in enumerate(regulations):
l = [regulation[k] for k in self.table_keys]
for j, obj in enumerate(l):
item = QTableWidgetItem()
item.setData(0, obj)
self.regulations_table.setItem(i, j, item)
def add_regulation(self):
rc = self.regulations_table.rowCount()
self.regulations_table.setRowCount(rc + 1)
for i, obj in enumerate(self.initial_values):
item = QTableWidgetItem()
item.setData(0, obj)
self.regulations_table.setItem(rc, i, item)
def remove_regulation(self):
self.regulations_table.removeRow(self.regulations_table.currentRow())
def get_value(self) -> List[Dict]:
l = []
for i in range(self.regulations_table.rowCount()):
dic = {}
for j in range(self.regulations_table.columnCount()):
item = self.regulations_table.item(i, j)
dic[self.table_keys[j]] = item.data(0)
l.append(dic)
return l
def set_value(self, value):
self.load_regulations(value)
class AddDataTableMixin(object):
""" Mixin providing validation and type casting for a table for adding cycle data.
Should be used as part of a widget that has a `table` attribute. If it
also has a `okButton`, this will be enabled/diabled when validation
is performed.
"""
invalid = Signal(int, int)
""" **signal** invalid(int `row`, int `col`)
Emitted if the data in cell `row`,`col` is invalid.
"""
def __init__(self, *args, emptyDateValid=True, **kwargs):
super().__init__(*args, **kwargs)
self.headerLabels = ['Date', 'Time', 'Distance (km)', 'Calories', 'Gear']
self.headerLabelColumnOffset = 0
self.table = QTableWidget(0, len(self.headerLabels))
self.table.setHorizontalHeaderLabels(self.headerLabels)
self.table.verticalHeader().setVisible(False)
# dict of methods to validate and cast types for input data in each column
isDatePartial = partial(isDate, allowEmpty=emptyDateValid)
validateMethods = [isDatePartial, isDuration, isFloat,
isFloat, isInt]
parseDatePartial = partial(parseDate, pd_timestamp=True)
castMethods = [parseDatePartial, parseDuration, float, float, int]
self.mthds = {name:{'validate':validateMethods[i], 'cast':castMethods[i]}
for i, name in enumerate(self.headerLabels)}
self.validateTimer = QTimer()
self.validateTimer.setInterval(100)
self.validateTimer.setSingleShot(True)
self.validateTimer.timeout.connect(self._validate)
self.table.cellChanged.connect(self.validateTimer.start)
self.invalid.connect(self._invalid)
@property
def defaultBrush(self):
# made this a property rather than setting in constructor as the mixin
# doesn't have a `table` attribute when __init__ is called
return self.table.item(0,0).background()
@property
def invalidBrush(self):
return QBrush(QColor("#910404"))
@Slot(int, int)
def _invalid(self, row, col):
""" Set the background of cell `row`,`col` to the `invalidBrush` and
disable the 'Ok' button.
"""
self.table.item(row, col).setBackground(self.invalidBrush)
if hasattr(self, "okButton"):
self.okButton.setEnabled(False)
@Slot()
def _validate(self):
""" Validate all data in the table.
If data is valid and the widget has an `okButton`, it will be enabled.
"""
# it would be more efficient to only validate a single cell, after its
# text has been changed, but this table is unlikely to ever be more
# than a few rows long, so this isn't too inefficient
allValid = True
for row in range(self.table.rowCount()):
for col, name in enumerate(self.headerLabels):
col += self.headerLabelColumnOffset
item = self.table.item(row, col)
value = item.text()
mthd = self.mthds[name]['validate']
valid = mthd(value)
if not valid:
if hasattr(self, "_clicked"):
if (row, col) not in self._clicked:
continue
self.invalid.emit(row, col)
allValid = False
elif valid and self.table.item(row, col).background() == self.invalidBrush:
self.table.item(row, col).setBackground(self.defaultBrush)
if allValid and hasattr(self, "okButton"):
self.okButton.setEnabled(True)
return allValid
def _getValues(self):
values = {name:[] for name in self.headerLabels}
self.table.sortItems(0, Qt.AscendingOrder)
for row in range(self.table.rowCount()):
for col, name in enumerate(self.headerLabels):
item = self.table.item(row, col)
value = item.text()
mthd = self.mthds[name]['cast']
value = mthd(value)
values[name].append(value)
return values
class D0(QGroupBox):
def __init__(self, parent=None):
self._parent = parent
super().__init__(parent)
self.setTitle("Define d₀")
layout = QVBoxLayout()
self.d0_grid_switch = QComboBox()
self.d0_grid_switch.addItems(["Constant", "Field"])
self.d0_grid_switch.currentTextChanged.connect(self.set_case)
layout.addWidget(self.d0_grid_switch)
self.d0_box = QWidget()
d0_box_layout = QHBoxLayout()
d0_box_layout.addWidget(QLabel("d₀"))
validator = QDoubleValidator()
validator.setBottom(0)
self.d0 = QLineEdit()
self.d0.setValidator(validator)
self.d0.editingFinished.connect(self.update_d0)
d0_box_layout.addWidget(self.d0)
d0_box_layout.addWidget(QLabel("Δd₀"))
self.d0e = QLineEdit()
self.d0e.setValidator(validator)
self.d0e.editingFinished.connect(self.update_d0)
d0_box_layout.addWidget(self.d0e)
self.d0_box.setLayout(d0_box_layout)
layout.addWidget(self.d0_box)
load_save = QWidget()
load_save_layout = QHBoxLayout()
self.load_grid = QPushButton("Load d₀ Grid")
self.load_grid.clicked.connect(self.load_d0_field)
load_save_layout.addWidget(self.load_grid)
self.save_grid = QPushButton("Save d₀ Grid")
self.save_grid.clicked.connect(self.save_d0_field)
load_save_layout.addWidget(self.save_grid)
load_save.setLayout(load_save_layout)
layout.addWidget(load_save)
self.d0_grid = QTableWidget()
self.d0_grid.setColumnCount(5)
self.d0_grid.setColumnWidth(0, 60)
self.d0_grid.setColumnWidth(1, 60)
self.d0_grid.setColumnWidth(2, 60)
self.d0_grid.setColumnWidth(3, 60)
self.d0_grid.verticalHeader().setVisible(False)
self.d0_grid.horizontalHeader().setStretchLastSection(True)
self.d0_grid.setHorizontalHeaderLabels(['vx', 'vy', 'vz', "d₀", "Δd₀"])
spinBoxDelegate = SpinBoxDelegate()
self.d0_grid.setItemDelegateForColumn(3, spinBoxDelegate)
self.d0_grid.setItemDelegateForColumn(4, spinBoxDelegate)
layout.addWidget(self.d0_grid)
self.setLayout(layout)
self.set_case('Constant')
def set_case(self, case):
if case == "Constant":
self.d0_box.setEnabled(True)
self.load_grid.setEnabled(False)
self.save_grid.setEnabled(False)
self.d0_grid.setEnabled(False)
else:
self.d0_box.setEnabled(False)
self.load_grid.setEnabled(True)
self.save_grid.setEnabled(True)
self.d0_grid.setEnabled(True)
def update_d0(self):
self._parent.update_plot()
def set_d0(self, d0, d0e):
if d0 is None:
self.d0.clear()
self.d0e.clear()
else:
self.d0.setText(str(d0))
self.d0e.setText(str(d0e))
def set_d0_field(self, x, y, z, d0, d0e):
if x is None:
self.d0_grid.clearContents()
else:
self.d0_grid.setRowCount(len(x))
for n in range(len(x)):
x_item = QTableWidgetItem(f'{x[n]: 7.2f}')
x_item.setFlags(x_item.flags() ^ Qt.ItemIsEditable)
y_item = QTableWidgetItem(f'{y[n]: 7.2f}')
y_item.setFlags(y_item.flags() ^ Qt.ItemIsEditable)
z_item = QTableWidgetItem(f'{z[n]: 7.2f}')
z_item.setFlags(z_item.flags() ^ Qt.ItemIsEditable)
d0_item = QTableWidgetItem()
d0_item.setData(Qt.EditRole, float(d0[n]))
d0e_item = QTableWidgetItem()
d0e_item.setData(Qt.EditRole, float(d0e[n]))
self.d0_grid.setItem(n, 0, QTableWidgetItem(x_item))
self.d0_grid.setItem(n, 1, QTableWidgetItem(y_item))
self.d0_grid.setItem(n, 2, QTableWidgetItem(z_item))
self.d0_grid.setItem(n, 3, QTableWidgetItem(d0_item))
self.d0_grid.setItem(n, 4, QTableWidgetItem(d0e_item))
def get_d0_field(self):
if self.d0_grid.rowCount() == 0:
return None
else:
x = [
float(self.d0_grid.item(row, 0).text())
for row in range(self.d0_grid.rowCount())
]
y = [
float(self.d0_grid.item(row, 1).text())
for row in range(self.d0_grid.rowCount())
]
z = [
float(self.d0_grid.item(row, 2).text())
for row in range(self.d0_grid.rowCount())
]
d0 = [
float(self.d0_grid.item(row, 3).text())
for row in range(self.d0_grid.rowCount())
]
d0e = [
float(self.d0_grid.item(row, 4).text())
for row in range(self.d0_grid.rowCount())
]
return (d0, d0e, x, y, z)
def save_d0_field(self):
filename, _ = QFileDialog.getSaveFileName(
self, "Save d0 Grid", "", "CSV (*.csv);;All Files (*)")
if filename:
d0, d0e, x, y, z = self.get_d0_field()
np.savetxt(filename,
np.array([x, y, z, d0, d0e]).T,
fmt=['%.4g', '%.4g', '%.4g', '%.9g', '%.9g'],
header="vx, vy, vz, d0, d0_error",
delimiter=',')
def load_d0_field(self):
filename, _ = QFileDialog.getOpenFileName(
self, "Load d0 Grid", "", "CSV (*.csv);;All Files (*)")
if filename:
x, y, z, d0, d0e = np.loadtxt(filename, delimiter=',', unpack=True)
self.set_d0_field(x, y, z, d0, d0e)
def get_d0(self):
if self.d0_grid_switch.currentText() == "Constant":
try:
return (float(self.d0.text()), float(self.d0e.text()))
except ValueError:
return None
else:
return self.get_d0_field()
class Extension2ReaderTable(QWidget):
"""Table showing extension to reader mappings with removal button.
Widget presented in preferences-plugin dialog."""
valueChanged = Signal(int)
def __init__(self, parent=None, npe2_readers=None, npe1_readers=None):
super().__init__(parent=parent)
npe2, npe1 = get_all_readers()
if npe2_readers is None:
npe2_readers = npe2
if npe1_readers is None:
npe1_readers = npe1
self._npe2_readers = npe2_readers
self._npe1_readers = npe1_readers
self._table = QTableWidget()
self._table.setShowGrid(False)
self._set_up_table()
self._edit_row = self._make_new_preference_row()
self._populate_table()
instructions = QLabel(
trans.
_('Enter a filename pattern to associate with a reader e.g. "*.tif" for all TIFF files.'
) + trans.
_('Available readers will be filtered to those compatible with your pattern. Hover over a reader to see what patterns it accepts.'
) + trans.
_('\n\nPreference saving for folder readers is not supported, so these readers are not shown.'
) + trans.
_('\n\nFor documentation on valid filename patterns, see https://docs.python.org/3/library/fnmatch.html'
))
instructions.setWordWrap(True)
instructions.setOpenExternalLinks(True)
layout = QVBoxLayout()
instructions.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Expanding)
layout.addWidget(instructions)
layout.addWidget(self._edit_row)
layout.addWidget(self._table)
self.setLayout(layout)
def _set_up_table(self):
"""Add table columns and headers, define styling"""
self._fn_pattern_col = 0
self._reader_col = 1
header_strs = [trans._('Filename Pattern'), trans._('Reader Plugin')]
self._table.setColumnCount(2)
self._table.setColumnWidth(self._fn_pattern_col, 200)
self._table.setColumnWidth(self._reader_col, 200)
self._table.verticalHeader().setVisible(False)
self._table.setMinimumHeight(120)
self._table.horizontalHeader().setStyleSheet(
'border-bottom: 2px solid white;')
self._table.setHorizontalHeaderLabels(header_strs)
self._table.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
def _populate_table(self):
"""Add row for each extension to reader mapping in settings"""
fnpattern2reader = get_settings().plugins.extension2reader
if len(fnpattern2reader) > 0:
for fn_pattern, plugin_name in fnpattern2reader.items():
self._add_new_row(fn_pattern, plugin_name)
else:
# Display that there are no filename patterns with reader associations
self._display_no_preferences_found()
def _make_new_preference_row(self):
"""Make row for user to add a new filename pattern assignment"""
edit_row_widget = QWidget()
edit_row_widget.setLayout(QGridLayout())
edit_row_widget.layout().setContentsMargins(0, 0, 0, 0)
self._fn_pattern_edit = QLineEdit()
self._fn_pattern_edit.setPlaceholderText(
"Start typing filename pattern...")
self._fn_pattern_edit.textChanged.connect(
self._filter_compatible_readers)
add_reader_widg = QWidget()
add_reader_widg.setLayout(QHBoxLayout())
add_reader_widg.layout().setContentsMargins(0, 0, 0, 0)
self._new_reader_dropdown = QComboBox()
for i, (plugin_name, display_name) in enumerate(
sorted(dict(self._npe2_readers,
**self._npe1_readers).items())):
self._add_reader_choice(i, plugin_name, display_name)
add_btn = QPushButton('Add')
add_btn.setToolTip(trans._('Save reader preference for pattern'))
add_btn.clicked.connect(self._save_new_preference)
add_reader_widg.layout().addWidget(self._new_reader_dropdown)
add_reader_widg.layout().addWidget(add_btn)
edit_row_widget.layout().addWidget(
self._fn_pattern_edit,
0,
0,
)
edit_row_widget.layout().addWidget(add_reader_widg, 0, 1)
return edit_row_widget
def _display_no_preferences_found(self):
self._table.setRowCount(1)
item = QTableWidgetItem(trans._('No filename preferences found.'))
item.setFlags(Qt.NoItemFlags)
self._table.setItem(self._fn_pattern_col, 0, item)
def _add_reader_choice(self, i, plugin_name, display_name):
"""Add dropdown item for plugin_name with reader pattern tooltip"""
reader_patterns = get_filename_patterns_for_reader(plugin_name)
# TODO: no reader_patterns means directory reader,
# we don't support preference association yet
if not reader_patterns:
return
self._new_reader_dropdown.addItem(display_name, plugin_name)
if '*' in reader_patterns:
tooltip_text = 'Accepts all'
else:
reader_patterns_formatted = ', '.join(sorted(
list(reader_patterns)))
tooltip_text = f'Accepts: {reader_patterns_formatted}'
self._new_reader_dropdown.setItemData(i,
tooltip_text,
role=Qt.ToolTipRole)
def _filter_compatible_readers(self, new_pattern):
"""Filter reader dropwdown items to those that accept `new_extension`"""
self._new_reader_dropdown.clear()
readers = self._npe2_readers.copy()
to_delete = []
compatible_readers = get_potential_readers(new_pattern)
for plugin_name, display_name in readers.items():
if plugin_name not in compatible_readers:
to_delete.append(plugin_name)
for reader in to_delete:
del readers[reader]
readers.update(self._npe1_readers)
if not readers:
self._new_reader_dropdown.addItem("None available")
else:
for i, (plugin_name,
display_name) in enumerate(sorted(readers.items())):
self._add_reader_choice(i, plugin_name, display_name)
def _save_new_preference(self, event):
"""Save current preference to settings and show in table"""
fn_pattern = self._fn_pattern_edit.text()
reader = self._new_reader_dropdown.currentData()
if not fn_pattern or not reader:
return
# if user types pattern that starts with a . it's probably a file extension so prepend the *
if fn_pattern.startswith('.'):
fn_pattern = f'*{fn_pattern}'
if fn_pattern in get_settings().plugins.extension2reader:
self._edit_existing_preference(fn_pattern, reader)
else:
self._add_new_row(fn_pattern, reader)
get_settings().plugins.extension2reader = {
**get_settings().plugins.extension2reader,
fn_pattern: reader,
}
def _edit_existing_preference(self, fn_pattern, reader):
"""Edit existing extension preference"""
current_reader_label = self.findChild(QLabel, fn_pattern)
if reader in self._npe2_readers:
reader = self._npe2_readers[reader]
current_reader_label.setText(reader)
def _add_new_row(self, fn_pattern, reader):
"""Add new reader preference to table"""
last_row = self._table.rowCount()
if (last_row == 1 and 'No filename preferences found'
in self._table.item(0, 0).text()):
self._table.removeRow(0)
last_row = 0
self._table.insertRow(last_row)
item = QTableWidgetItem(fn_pattern)
item.setFlags(Qt.NoItemFlags)
self._table.setItem(last_row, self._fn_pattern_col, item)
plugin_widg = QWidget()
# need object name to easily find row
plugin_widg.setObjectName(f'{fn_pattern}')
plugin_widg.setLayout(QHBoxLayout())
plugin_widg.layout().setContentsMargins(0, 0, 0, 0)
if reader in self._npe2_readers:
reader = self._npe2_readers[reader]
plugin_label = QLabel(reader, objectName=fn_pattern)
# need object name to easily work out which button was clicked
remove_btn = QPushButton('X', objectName=fn_pattern)
remove_btn.setFixedWidth(30)
remove_btn.setStyleSheet('margin: 4px;')
remove_btn.setToolTip(
trans._('Remove this filename pattern to reader association'))
remove_btn.clicked.connect(self.remove_existing_preference)
plugin_widg.layout().addWidget(plugin_label)
plugin_widg.layout().addWidget(remove_btn)
self._table.setCellWidget(last_row, self._reader_col, plugin_widg)
def remove_existing_preference(self, event):
"""Delete extension to reader mapping setting and remove table row"""
pattern_to_remove = self.sender().objectName()
current_settings = get_settings().plugins.extension2reader
# need explicit assignment to new object here for persistence
get_settings().plugins.extension2reader = {
k: v
for k, v in current_settings.items() if k != pattern_to_remove
}
for i in range(self._table.rowCount()):
row_widg_name = self._table.cellWidget(
i, self._reader_col).objectName()
if row_widg_name == pattern_to_remove:
self._table.removeRow(i)
break
if self._table.rowCount() == 0:
self._display_no_preferences_found()
def value(self):
"""Return extension:reader mapping from settings.
Returns
-------
Dict[str, str]
mapping of extension to reader plugin display name
"""
return get_settings().plugins.extension2reader
class DialogSelectQuantStandard(QDialog):
def __init__(self, parent=None):
super().__init__(parent)
self._qe_param_built_in = []
self._qe_param_custom = []
self._qe_standard_selected = None
self._qe_param = [] # The list of all standards
self._custom_label = [] # The list of booleans: True - the standard is custom, False -built-in
self.setWindowTitle("Load Quantitative Standard")
self.setMinimumHeight(500)
self.setMinimumWidth(600)
self.resize(600, 500)
self.selected_standard_index = -1
labels = ("C", "Serial #", "Name", "Description")
col_stretch = (
QHeaderView.ResizeToContents,
QHeaderView.ResizeToContents,
QHeaderView.ResizeToContents,
QHeaderView.Stretch,
)
self.table = QTableWidget()
set_tooltip(
self.table,
"To <b> load the sta"
"ndard</b>, double-click on the table row or "
"select the table row and then click <b>Ok</b> button.",
)
self.table.setMinimumHeight(200)
self.table.setColumnCount(len(labels))
self.table.verticalHeader().hide()
self.table.setHorizontalHeaderLabels(labels)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.itemSelectionChanged.connect(self.item_selection_changed)
self.table.itemDoubleClicked.connect(self.item_double_clicked)
self.table.setStyleSheet(
"QTableWidget::item{color: black;}"
"QTableWidget::item:selected{background-color: red;}"
"QTableWidget::item:selected{color: white;}"
)
header = self.table.horizontalHeader()
for n, col_stretch in enumerate(col_stretch):
# Set stretching for the columns
header.setSectionResizeMode(n, col_stretch)
self.lb_info = QLabel()
self.lb_info.setText("Column 'C': * means that the standard is user-defined.")
button_box = QDialogButtonBox(QDialogButtonBox.Open | QDialogButtonBox.Cancel)
button_box.button(QDialogButtonBox.Cancel).setDefault(True)
button_box.accepted.connect(self.accept)
button_box.rejected.connect(self.reject)
self.pb_open = button_box.button(QDialogButtonBox.Open)
self.pb_open.setEnabled(False)
vbox = QVBoxLayout()
vbox.addWidget(self.table)
vbox.addWidget(self.lb_info)
vbox.addWidget(button_box)
self.setLayout(vbox)
def _fill_table(self, table_contents):
self.table.setRowCount(len(table_contents))
for nr, row in enumerate(table_contents):
for nc, entry in enumerate(row):
s = textwrap.fill(entry, width=40)
item = QTableWidgetItem(s)
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
if not nc:
item.setTextAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.table.setItem(nr, nc, item)
self.table.resizeRowsToContents()
brightness = 220
for nr in range(self.table.rowCount()):
for nc in range(self.table.columnCount()):
self.table.item(nr, nc)
if nr % 2:
color = QColor(255, brightness, brightness)
else:
color = QColor(brightness, 255, brightness)
self.table.item(nr, nc).setBackground(QBrush(color))
try:
index = self._qe_param.index(self._qe_standard_selected)
self.selected_standard_index = index
n_columns = self.table.columnCount()
self.table.setRangeSelected(QTableWidgetSelectionRange(index, 0, index, n_columns - 1), True)
except ValueError:
pass
def item_selection_changed(self):
sel_ranges = self.table.selectedRanges()
# The table is configured to have one or no selected ranges
# 'Open' button should be enabled only if a range (row) is selected
if sel_ranges:
self.selected_standard_index = sel_ranges[0].topRow()
self.pb_open.setEnabled(True)
else:
self.selected_standard_index = -1
self.pb_open.setEnabled(False)
def item_double_clicked(self):
self.accept()
def set_standards(self, qe_param_built_in, qe_param_custom, qe_standard_selected):
self._qe_standard_selected = qe_standard_selected
self._qe_param = qe_param_custom + qe_param_built_in
custom_label = [True] * len(qe_param_custom) + [False] * len(qe_param_built_in)
table_contents = []
for n, param in enumerate(self._qe_param):
custom = "*" if custom_label[n] else ""
serial = param["serial"]
name = param["name"]
description = param["description"]
table_contents.append([custom, serial, name, description])
self._fill_table(table_contents)
def get_selected_standard(self):
if self.selected_standard_index >= 0:
return self._qe_param[self.selected_standard_index]
else:
return None