def setCurvatureKymographLUT(self, lut_string):
from ij import IJ
if lut_string in IJ.getLuts():
self.curvature_kymograph_lut_string = lut_string
else:
raise ValueError(
'Requested curvature kymograph LUT is not a valid IJ LUT')
def setActinKymographLUT(self, lut_string):
from ij import IJ
if lut_string in IJ.getLuts():
self.actin_kymograph_lut_string = lut_string
else:
raise ValueError(
'Requested actin kymograph LUT is not a valid IJ LUT')
def setCurvatureOverlayLUT(self, lut_string):
from ij import IJ
if lut_string in IJ.getLuts():
self.curvature_overlay_lut_string = lut_string
else:
raise ValueError(
'Requested curvature overlay LUT is not a valid IJ LUT')
def analysis_parameters_gui(rerun_analysis=False, params=None):
"""GUI for setting analysis parameters at the start of a run. TODO: more effectively separate model and view"""
if params is None:
params = Parameters(load_last_params = True);
dialog = GenericDialog("Analysis parameters");
controls = [];
if rerun_analysis:
params.setUseSingleChannel(False);
params.togglePerformUserQC(False);
params.setDoInnerOuterComparison(False);
controls.append(MyControlDefinition(u'Curvature length parameter (\u00b5m): ',
MyControlDefinition.Numeric,
round(params.curvature_length_um, 2),
params.setCurvatureLengthUm));
controls.append(MyControlDefinition(u'Width of region for intensity analysis (\u00b5m): ',
MyControlDefinition.Numeric,
round(params.intensity_profile_width_um, 2),
params.setIntensityProfileWidthUm))
controls.append(MyControlDefinition("Threshold method: ",
MyControlDefinition.Choice,
params.threshold_method,
params.setThresholdMethod,
choices=params.listThresholdMethods(),
enabled=(not rerun_analysis)));
controls.append(MyControlDefinition("Curvature overlay LUT: ",
MyControlDefinition.Choice,
params.curvature_overlay_lut_string,
params.setCurvatureOverlayLUT,
choices=IJ.getLuts()));
controls.append(MyControlDefinition("Curvature kymograph LUT: ",
MyControlDefinition.Choice,
params.curvature_kymograph_lut_string,
params.setCurvatureKymographLUT,
choices=IJ.getLuts()));
controls.append(MyControlDefinition("Labelled species kymograph LUT: ",
MyControlDefinition.Choice,
params.actin_kymograph_lut_string,
params.setActinKymographLUT,
choices=IJ.getLuts()));
controls.append(MyControlDefinition("Labelled species for intensity analysis: ",
MyControlDefinition.String,
params.labeled_species,
params.setLabeledSpecies));
controls.append(MyControlDefinition("Use intensity channel for segmentation too?",
MyControlDefinition.Checkbox,
params.use_single_channel,
params.setUseSingleChannel,
enabled=(not rerun_analysis)));
controls.append(MyControlDefinition("Metadata source: ",
MyControlDefinition.RadioButtonGroup,
params.metadata_source,
params.setMetadataSource,
choices=["Image metadata", "Acquisition metadata"]));
controls.append(MyControlDefinition("Constrain anchors close to manual selections?",
MyControlDefinition.Checkbox,
params.constrain_anchors,
params.toggleConstrainAnchors,
enabled=(not rerun_analysis)));
controls.append(MyControlDefinition("Filter out negative curvatures",
MyControlDefinition.Checkbox,
params.filter_negative_curvatures,
params.setFilterNegativeCurvatures));
controls.append(MyControlDefinition("Account for photobleaching?",
MyControlDefinition.Checkbox,
params.photobleaching_correction,
params.togglePhotobleachingCorrection));
controls.append(MyControlDefinition("Perform quality control of membrane edges?",
MyControlDefinition.Checkbox,
params.perform_user_qc,
params.togglePerformUserQC,
enabled=(not rerun_analysis)));
controls.append(MyControlDefinition("Perform quality control of background regions?",
MyControlDefinition.Checkbox,
params.qc_background_rois,
params.toggleBackgroundQc));
controls.append(MyControlDefinition("Perform spatial cropping?",
MyControlDefinition.Checkbox,
params.perform_spatial_crop,
params.toggleSpatialCrop,
enabled=(not rerun_analysis)));
controls.append(MyControlDefinition("Perform time cropping?",
MyControlDefinition.Checkbox,
params.perform_time_crop,
params.toggleTimeCrop,
enabled=(not rerun_analysis)));
controls.append(MyControlDefinition("Close images on completion?",
MyControlDefinition.Checkbox,
params.close_on_completion,
params.toggleCloseOnCompletion));
controls.append(MyControlDefinition("Compare inner and outer curvature regions?",
MyControlDefinition.Checkbox,
params.inner_outer_comparison,
params.setDoInnerOuterComparison,
enabled=(not rerun_analysis)));
for control in controls:
control.addControl(dialog);
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
numeric_controls = [c for c in controls if c.control_type==MyControlDefinition.Numeric];
for nc, nf in zip(numeric_controls, dialog.getNumericFields()):
nc.setter(float(nf.getText()));
string_controls = [c for c in controls if c.control_type==MyControlDefinition.String];
for sc, sf in zip(string_controls, dialog.getStringFields()):
sc.setter(sf.getText());
choice_controls = [c for c in controls if c.control_type==MyControlDefinition.Choice];
for cc, cf in zip(choice_controls, dialog.getChoices()):
cc.setter(cf.getSelectedItem());
checkbox_controls = [c for c in controls if c.control_type==MyControlDefinition.Checkbox];
for cbc, cbf in zip(checkbox_controls, dialog.getCheckboxes()):
cbc.setter(cbf.getState());
radiobuttongroup_controls = [c for c in controls if c.control_type==MyControlDefinition.RadioButtonGroup];
for rbc in radiobuttongroup_controls:
rbc.setter(rbc.checkboxes[[cb.getState() for cb in rbc.checkboxes].index(True)].getLabel());
params.persistParameters();
return params;