class FindspotsSimplerParameterTab(QWidget):
"""
This widget is the tool for tunning the simpler and most common parameters
in the spot-finder, this widget is the first to appear once the button
"Find Sots" at the left side of the GUI is clicked
"""
item_changed = Signal(str, str)
def __init__(self, parent=None):
super(FindspotsSimplerParameterTab, self).__init__()
# self.param_widget_parent = parent.param_widget_parent
#TODO thinks about making "None equivalent to 1"
xds_gain_label = QLabel("Gain")
xds_gain_spn_bx = QDoubleSpinBox()
xds_gain_spn_bx.local_path = "spotfinder.threshold.dispersion.gain"
xds_gain_spn_bx.setSpecialValueText("None")
xds_gain_spn_bx.setValue(1.0)
xds_gain_spn_bx.valueChanged.connect(self.spnbox_changed)
xds_sigma_background_label = QLabel("Sigma Background")
xds_sigma_background_spn_bx = QDoubleSpinBox()
xds_sigma_background_spn_bx.setValue(6.0)
xds_sigma_background_spn_bx.local_path = (
"spotfinder.threshold.dispersion.sigma_background")
xds_sigma_background_spn_bx.valueChanged.connect(self.spnbox_changed)
xds_sigma_strong_label = QLabel("Sigma Strong")
xds_sigma_strong_spn_bx = QDoubleSpinBox()
xds_sigma_strong_spn_bx.setValue(3.0)
xds_sigma_strong_spn_bx.local_path = (
"spotfinder.threshold.dispersion.sigma_strong")
xds_sigma_strong_spn_bx.valueChanged.connect(self.spnbox_changed)
xds_global_threshold_label = QLabel("Global Threshold")
xds_global_threshold_spn_bx = QDoubleSpinBox()
xds_global_threshold_spn_bx.local_path = (
"spotfinder.threshold.dispersion.global_threshold")
xds_global_threshold_spn_bx.valueChanged.connect(self.spnbox_changed)
localLayout = QVBoxLayout()
xds_gain_hb = QHBoxLayout()
xds_gain_hb.addWidget(xds_gain_label)
xds_gain_hb.addWidget(xds_gain_spn_bx)
localLayout.addLayout(xds_gain_hb)
xds_sigma_background_hb = QHBoxLayout()
xds_sigma_background_hb.addWidget(xds_sigma_background_label)
xds_sigma_background_hb.addWidget(xds_sigma_background_spn_bx)
localLayout.addLayout(xds_sigma_background_hb)
xds_sigma_strong_hb = QHBoxLayout()
xds_sigma_strong_hb.addWidget(xds_sigma_strong_label)
xds_sigma_strong_hb.addWidget(xds_sigma_strong_spn_bx)
localLayout.addLayout(xds_sigma_strong_hb)
xds_global_threshold_hb = QHBoxLayout()
xds_global_threshold_hb.addWidget(xds_global_threshold_label)
xds_global_threshold_hb.addWidget(xds_global_threshold_spn_bx)
localLayout.addLayout(xds_global_threshold_hb)
hbox_lay_nproc = QHBoxLayout()
label_nproc = QLabel("Number of Jobs")
# label_nproc.setPalette(palette_object)
# label_nproc.setFont( QFont("Monospace", 10))
hbox_lay_nproc.addWidget(label_nproc)
self.box_nproc = QSpinBox()
self.box_nproc.local_path = "spotfinder.mp.nproc"
self.box_nproc.valueChanged.connect(self.spnbox_changed)
hbox_lay_nproc.addWidget(self.box_nproc)
localLayout.addLayout(hbox_lay_nproc)
self.inner_reset_btn = ResetButton()
localLayout.addWidget(self.inner_reset_btn)
localLayout.addStretch()
self.setLayout(localLayout)
self.lst_var_widg = _get_all_direct_layout_widget_children(localLayout)
def spnbox_changed(self, value):
sender = self.sender()
str_value = str(value)
logger.debug(value)
str_path = str(sender.local_path)
# self.param_widget_parent.update_lin_txt(str_path, str_value)
self.item_changed.emit(str_path, str_value)
def set_max_nproc(self):
cpu_max_proc = int(libtbx.introspection.number_of_processors())
self.box_nproc.setValue(cpu_max_proc)
return cpu_max_proc
class IntegrateSimplerParamTab(SimpleParamTab):
"""
This widget is the tool for tunning the simpler and most common parameters
in the integrate algorithm, this widget is the first to appear once the button
"Integrate" at the left side of the GUI is clicked
"""
def __init__(self, parent=None):
super(IntegrateSimplerParamTab, self).__init__()
# self.param_widget_parent = parent.param_widget_parent
localLayout = QVBoxLayout()
PrFit_lay_out = QHBoxLayout()
label_PrFit = QLabel("Use profile fitting")
PrFit_lay_out.addWidget(label_PrFit)
PrFit_comb_bx = DefaultComboBox("integration.profile.fitting",
["True", "False", "Auto"])
PrFit_comb_bx.currentIndexChanged.connect(self.combobox_changed)
PrFit_lay_out.addWidget(PrFit_comb_bx)
localLayout.addLayout(PrFit_lay_out)
hbox_lay_algorithm_53 = QHBoxLayout()
label_algorithm_53 = QLabel("Background algorithm")
hbox_lay_algorithm_53.addWidget(label_algorithm_53)
box_algorithm_53 = DefaultComboBox(
"integration.background.algorithm",
["simple", "null", "median", "gmodel", "glm"],
default_index=4)
box_algorithm_53.currentIndexChanged.connect(self.combobox_changed)
hbox_lay_algorithm_53.addWidget(box_algorithm_53)
localLayout.addLayout(hbox_lay_algorithm_53)
hbox_d_min = QHBoxLayout()
label_d_min = QLabel("High resolution limit")
hbox_d_min.addWidget(label_d_min)
d_min_spn_bx = QDoubleSpinBox()
d_min_spn_bx.local_path = "prediction.d_min"
d_min_spn_bx.setSpecialValueText("None")
d_min_spn_bx.setValue(0.0)
hbox_d_min.addWidget(d_min_spn_bx)
d_min_spn_bx.editingFinished.connect(self.spnbox_finished)
localLayout.addLayout(hbox_d_min)
hbox_lay_nproc = QHBoxLayout()
label_nproc = QLabel("Number of jobs")
# label_nproc.setFont( QFont("Monospace", 10))
hbox_lay_nproc.addWidget(label_nproc)
self.box_nproc = QSpinBox()
self.box_nproc.local_path = "integration.mp.nproc"
self.box_nproc.editingFinished.connect(self.spnbox_finished)
hbox_lay_nproc.addWidget(self.box_nproc)
localLayout.addLayout(hbox_lay_nproc)
self.inner_reset_btn = ResetButton()
localLayout.addWidget(self.inner_reset_btn)
localLayout.addStretch()
self.setLayout(localLayout)
self.box_nproc.tmp_lst = None
self.lst_var_widg = _get_all_direct_layout_widget_children(localLayout)
def set_max_nproc(self):
cpu_max_proc = int(libtbx.introspection.number_of_processors())
self.box_nproc.setValue(cpu_max_proc)
return cpu_max_proc
class IntegrateSimplerParamTab(QWidget):
"""
This widget is the tool for tunning the simpler and most common parameters
in the integrate algorithm, this widget is the first to appear once the button
"Integrate" at the left side of the GUI is clicked
"""
item_changed = Signal(str, str)
def __init__(self, parent=None):
super(IntegrateSimplerParamTab, self).__init__()
# self.param_widget_parent = parent.param_widget_parent
localLayout = QVBoxLayout()
PrFit_lay_out = QHBoxLayout()
label_PrFit = QLabel("Use Profile Fitting")
PrFit_lay_out.addWidget(label_PrFit)
PrFit_comb_bx = QComboBox()
PrFit_comb_bx.local_path = "integration.profile.fitting"
PrFit_comb_bx.tmp_lst = []
PrFit_comb_bx.tmp_lst.append("True")
PrFit_comb_bx.tmp_lst.append("False")
PrFit_comb_bx.tmp_lst.append("Auto")
for lst_itm in PrFit_comb_bx.tmp_lst:
PrFit_comb_bx.addItem(lst_itm)
PrFit_comb_bx.currentIndexChanged.connect(self.combobox_changed)
PrFit_lay_out.addWidget(PrFit_comb_bx)
localLayout.addLayout(PrFit_lay_out)
hbox_lay_algorithm_53 = QHBoxLayout()
label_algorithm_53 = QLabel("Background Algorithm")
hbox_lay_algorithm_53.addWidget(label_algorithm_53)
box_algorithm_53 = QComboBox()
box_algorithm_53.local_path = "integration.background.algorithm"
box_algorithm_53.tmp_lst = []
box_algorithm_53.tmp_lst.append("simple")
box_algorithm_53.tmp_lst.append("null")
box_algorithm_53.tmp_lst.append("median")
box_algorithm_53.tmp_lst.append("gmodel")
box_algorithm_53.tmp_lst.append("glm")
for lst_itm in box_algorithm_53.tmp_lst:
box_algorithm_53.addItem(lst_itm)
box_algorithm_53.setCurrentIndex(4)
box_algorithm_53.currentIndexChanged.connect(self.combobox_changed)
hbox_lay_algorithm_53.addWidget(box_algorithm_53)
localLayout.addLayout(hbox_lay_algorithm_53)
hbox_d_min = QHBoxLayout()
label_d_min = QLabel("d_min")
hbox_d_min.addWidget(label_d_min)
d_min_spn_bx = QDoubleSpinBox()
d_min_spn_bx.local_path = "prediction.d_min"
d_min_spn_bx.setSpecialValueText("None")
d_min_spn_bx.setValue(0.0)
hbox_d_min.addWidget(d_min_spn_bx)
d_min_spn_bx.valueChanged.connect(self.spnbox_changed)
localLayout.addLayout(hbox_d_min)
hbox_lay_nproc = QHBoxLayout()
label_nproc = QLabel("Number of Jobs")
# label_nproc.setFont( QFont("Monospace", 10))
hbox_lay_nproc.addWidget(label_nproc)
self.box_nproc = QSpinBox()
self.box_nproc.local_path = "integration.mp.nproc"
self.box_nproc.valueChanged.connect(self.spnbox_changed)
hbox_lay_nproc.addWidget(self.box_nproc)
localLayout.addLayout(hbox_lay_nproc)
self.inner_reset_btn = ResetButton()
localLayout.addWidget(self.inner_reset_btn)
localLayout.addStretch()
self.setLayout(localLayout)
self.box_nproc.tmp_lst = None
self.lst_var_widg = _get_all_direct_layout_widget_children(localLayout)
def combobox_changed(self, value):
sender = self.sender()
str_value = str(sender.tmp_lst[value])
str_path = str(sender.local_path)
# self.param_widget_parent.update_lin_txt(str_path, str_value)
self.item_changed.emit(str_path, str_value)
def spnbox_changed(self, value):
sender = self.sender()
str_value = str(value)
logger.debug(value)
str_path = str(sender.local_path)
self.item_changed.emit(str_path, str_value)
def set_max_nproc(self):
cpu_max_proc = int(libtbx.introspection.number_of_processors())
self.box_nproc.setValue(cpu_max_proc)
return cpu_max_proc
class ImportPage(QWidget):
update_command_lst_low_level = Signal(list)
"""
This stacked widget basically helps the user to browse the input images
path, there is no auto-generated GUI form Phil parameters in use withing
this widget.
"""
def __init__(self, parent=None):
super(ImportPage, self).__init__(parent=None)
main_v_box = QVBoxLayout()
label_font = QFont()
sys_font_point_size = label_font.pointSize()
label_font.setPointSize(sys_font_point_size + 2)
step_label = QLabel(str("Import"))
step_label.setFont(label_font)
self.simple_lin = QLineEdit(self)
self.simple_lin.textChanged.connect(self.update_command)
self.x_spn_bx = QSpinBox()
self.x_spn_bx.setMaximum(99999)
self.x_spn_bx.setSpecialValueText(" ")
self.y_spn_bx = QSpinBox()
self.y_spn_bx.setMaximum(99999)
self.y_spn_bx.setSpecialValueText(" ")
self.x_spn_bx.valueChanged.connect(self.x_beam_changed)
self.y_spn_bx.valueChanged.connect(self.y_beam_changed)
self.chk_invert = QCheckBox("Invert rotation axis")
self.chk_invert.stateChanged.connect(self.inv_rota_changed)
self.opn_fil_btn = QPushButton(" \n Select file(s) \n ")
main_path = get_main_path()
self.opn_fil_btn.setIcon(QIcon(main_path + "/resources/import.png"))
self.opn_fil_btn.setIconSize(QSize(80, 48))
main_v_box.addWidget(step_label)
main_v_box.addWidget(self.opn_fil_btn)
main_v_box.addWidget(self.simple_lin)
self.b_cetre_label = QLabel("\n\n Beam centre")
main_v_box.addWidget(self.b_cetre_label)
cent_hbox = QHBoxLayout()
self.x_label = QLabel(" X: ")
cent_hbox.addWidget(self.x_label)
cent_hbox.addWidget(self.x_spn_bx)
self.y_label = QLabel(" Y: ")
cent_hbox.addWidget(self.y_label)
cent_hbox.addWidget(self.y_spn_bx)
# cent_hbox.addWidget(QLabel(" \n "))
cent_hbox.addStretch()
main_v_box.addLayout(cent_hbox)
main_v_box.addWidget(self.chk_invert)
main_v_box.addStretch()
self.opn_fil_btn.clicked.connect(self.open_files)
self.defa_dir = str(os.getcwd())
self.setLayout(main_v_box)
# self.show()
self.reset_par()
def reset_par(self):
logger.info("reset_par(ImportPage)")
self.cmd_list = []
self.simple_lin.setText(" ? ")
self.x_spn_bx.setValue(0.0)
self.y_spn_bx.setValue(0.0)
self.chk_invert.setChecked(False)
self.x_beam, self.y_beam = 0.0, 0.0
self.path_file_str = ""
self.second_half = ""
self.third_half = ""
def update_param_w_lst(self, lst_in):
self.reset_par()
logger.info("update_param_w_lst(ImportPage) \n lst: \n", lst_in)
for singl_com in lst_in:
if singl_com[0:1] == "/":
self.path_file_str = str(singl_com)
self.put_str_lin()
if singl_com[0:12] == "image_range=":
self.path_file_str += " "
self.path_file_str += str(singl_com)
self.put_str_lin()
if singl_com == "invert_rotation_axis=True":
self.chk_invert.setChecked(True)
if singl_com[0:22] == "slow_fast_beam_centre=":
yb_xb_str = singl_com[22:]
yb_str, xb_str = yb_xb_str.split(",")
yb = float(yb_str)
xb = float(xb_str)
self.y_spn_bx.setValue(yb)
self.x_spn_bx.setValue(xb)
def inv_rota_changed(self):
if self.chk_invert.checkState():
self.third_half = "invert_rotation_axis=True"
else:
self.third_half = ""
self.put_str_lin()
def x_beam_changed(self, value):
self.x_beam = value
self.build_second_half()
def y_beam_changed(self, value):
self.y_beam = value
self.build_second_half()
def build_second_half(self):
if self.x_beam != 0.0 and self.y_beam != 0.0:
self.second_half = (
"slow_fast_beam_centre=" + str(self.y_beam) + "," + str(self.x_beam)
)
else:
self.second_half = ""
self.put_str_lin()
def open_files(self):
lst_file_path = QFileDialog.getOpenFileNames(
self, "Open File(s)", self.defa_dir, "All Files (*.*)"
)
if len(lst_file_path) > 0:
new_dir, new_command = get_import_run_string(lst_file_path)
# logger.info("\n new_dir=", new_dir, ">>")
# logger.info("\n new_command =", new_command, ">>")
self.path_file_str = new_command
self.defa_dir = new_dir
self.put_str_lin()
def put_str_lin(self):
# logger.info("self.path_file_str =", self.path_file_str, ">>")
self.cmd_list = [
self.path_file_str,
self.second_half.lstrip(),
self.third_half.lstrip(),
]
txt_lin = " ".join(self.cmd_list).rstrip()
while " " in txt_lin:
txt_lin = txt_lin.replace(" ", " ")
self.simple_lin.setText(txt_lin)
def set_arg_obj(self, sys_arg_in):
"""Pass the system argument object to handle launch arguments."""
if sys_arg_in.template is not None:
str_arg = str(sys_arg_in.template)
self.simple_lin.setText(str_arg)
def update_command(self):
self.command_lst = [["import"]]
param_com = str(self.simple_lin.text())
cmd_lst = param_com.split(" ")
for single_com in cmd_lst:
self.command_lst[0].append(single_com)
self.update_command_lst_low_level.emit(self.command_lst[0])
def gray_me_out(self):
self.simple_lin.setEnabled(False)
self.opn_fil_btn.setEnabled(False)
self.x_spn_bx.setEnabled(False)
self.y_spn_bx.setEnabled(False)
self.x_label.setEnabled(False)
self.y_label.setEnabled(False)
self.b_cetre_label.setEnabled(False)
self.chk_invert.setEnabled(False)
def activate_me(self, cur_nod=None):
self.simple_lin.setEnabled(True)
self.opn_fil_btn.setEnabled(True)
self.y_spn_bx.setEnabled(True)
self.x_spn_bx.setEnabled(True)
self.x_label.setEnabled(True)
self.y_label.setEnabled(True)
self.b_cetre_label.setEnabled(True)
self.chk_invert.setEnabled(True)
