Index

A

AcquisitionDims (class in darfix.core.dataset) add_dim() (darfix.core.dataset.Dataset method) addDim() (darfix.gui.dimensionsWidget.DimensionMapping method) (darfix.gui.dimensionsWidget.DimensionWidget method) addFile() (darfix.gui.datasetSelectionWidget.FilesSelectionWidget method) apply() (darfix.gui.roiSelectionWidget.ROISelectionWidget method) apply_2D_ROI() (in module darfix.core.roi)

apply_3D_ROI() (in module darfix.core.roi) apply_background_subtraction() (darfix.core.dataset.Dataset method) apply_funcs() (darfix.core.dataset.Data method) apply_hot_pixel_removal() (darfix.core.dataset.Dataset method) apply_roi() (darfix.core.dataset.Dataset method) apply_shift() (darfix.core.dataset.Dataset method) (in module darfix.core.imageRegistration) applyRoi() (darfix.gui.roiSelectionWidget.ROISelectionWidget method)

B

background_subtraction() (in module darfix.core.imageOperations) background_subtraction_2D() (in module darfix.core.imageOperations)

Base (class in darfix.decomposition.base) BSSWidget (class in darfix.gui.blindSourceSeparationWidget)

C

chunk_image() (in module darfix.core.imageOperations) clearStack() (darfix.gui.roiSelectionWidget.ROISelectionWidget method) Component (class in darfix.core.componentsMatching) ComponentsMatching (class in darfix.core.componentsMatching)

compute_com() (in module darfix.core.imageRegistration) compute_frames_intensity() (darfix.core.dataset.Dataset method) convert_to_hdf5() (darfix.core.dataset.Data method) correct() (darfix.gui.shiftCorrectionWidget.ShiftCorrectionWidget method) crossover() (darfix.core.geneticShiftDetection.GeneticShiftDetection method)

D

darfix.core.componentsMatching (module) darfix.core.dataset (module) darfix.core.geneticShiftDetection (module) darfix.core.imageOperations (module) darfix.core.imageRegistration (module) darfix.core.roi (module) darfix.decomposition.base (module) darfix.decomposition.ipca (module) darfix.decomposition.nica (module) darfix.decomposition.nmf (module) darfix.gui.blindSourceSeparationWidget (module) darfix.gui.dataPartitionWidget (module) darfix.gui.datasetSelectionWidget (module) darfix.gui.dimensionsWidget (module) darfix.gui.displayComponentsWidget (module)

darfix.gui.linkComponentsWidget (module) darfix.gui.metadataWidget (module) darfix.gui.noiseRemovalWidget (module) darfix.gui.PCAWidget (module) darfix.gui.roiSelectionWidget (module) darfix.gui.shiftCorrectionWidget (module) Data (class in darfix.core.dataset) DataPartitionWidget (class in darfix.gui.dataPartitionWidget) Dataset (class in darfix.core.dataset) DatasetSelectionWidget (class in darfix.gui.datasetSelectionWidget) diff_com() (in module darfix.core.imageRegistration) Dimension (class in darfix.core.dataset) DimensionMapping (class in darfix.gui.dimensionsWidget) DimensionWidget (class in darfix.gui.dimensionsWidget) DisplayComponentsWidget (class in darfix.gui.displayComponentsWidget) draw_matches() (darfix.core.componentsMatching.ComponentsMatching method)

E

euclidean_distance() (darfix.core.componentsMatching.ComponentsMatching method)

F

FilenameSelectionWidget (class in darfix.gui.datasetSelectionWidget) FilesSelectionWidget (class in darfix.gui.datasetSelectionWidget) find_and_apply_shift() (darfix.core.dataset.Dataset method) find_dimensions() (darfix.core.dataset.Dataset method) find_shift() (darfix.core.dataset.Dataset method) (in module darfix.core.imageRegistration) fit() (darfix.core.geneticShiftDetection.GeneticShiftDetection method) (darfix.gui.dimensionsWidget.DimensionWidget method) fit_transform() (darfix.decomposition.base.Base method) (darfix.decomposition.ipca.IPCA method) (darfix.decomposition.nica.NICA method) (darfix.decomposition.nmf.NMF method)

fitFailed (darfix.gui.dimensionsWidget.DimensionMapping attribute) fitness() (darfix.core.geneticShiftDetection.GeneticShiftDetection method) fitSucceed (darfix.gui.dimensionsWidget.DimensionMapping attribute) flatten() (darfix.core.dataset.Data method) frobenius_norm() (darfix.decomposition.base.Base method) from_dict() (darfix.core.dataset.AcquisitionDims method) (darfix.core.dataset.Dimension static method)

G

generate() (darfix.core.geneticShiftDetection.GeneticShiftDetection method) GeneticShiftDetection (class in darfix.core.geneticShiftDetection) get() (darfix.core.dataset.AcquisitionDims method) get_data() (darfix.core.dataset.Dataset method)

get_dimensions_values() (darfix.core.dataset.Dataset method) get_names() (darfix.core.dataset.AcquisitionDims method) getRoi() (darfix.gui.roiSelectionWidget.ROISelectionWidget method) getStack() (darfix.gui.shiftCorrectionWidget.ShiftCorrectionWidget method)

H

hot_pixel_removal_2D() (in module darfix.core.imageOperations)

hot_pixel_removal_3D() (in module darfix.core.imageOperations)

I

img2img_mean() (in module darfix.core.imageOperations) improve_linear_shift() (in module darfix.core.imageRegistration)

initialize() (darfix.core.geneticShiftDetection.GeneticShiftDetection method) IPCA (class in darfix.decomposition.ipca)

L

LinkComponentsWidget (class in darfix.gui.linkComponentsWidget)

loadDataset() (darfix.gui.datasetSelectionWidget.DatasetSelectionWidget method)

M

match_components() (darfix.core.componentsMatching.ComponentsMatching method) MetadataWidget (class in darfix.gui.metadataWidget) Method (class in darfix.core.componentsMatching) (class in darfix.core.imageOperations) (class in darfix.gui.blindSourceSeparationWidget)

mutate() (darfix.core.geneticShiftDetection.GeneticShiftDetection method)

N

ndim() (darfix.core.dataset.Data property) nframes() (darfix.core.dataset.Dataset property) NICA (class in darfix.decomposition.nica) nica() (darfix.core.dataset.Dataset method) nica_nmf() (darfix.core.dataset.Dataset method)

NMF (class in darfix.decomposition.nmf) nmf() (darfix.core.dataset.Dataset method) NoiseRemovalDialog (class in darfix.gui.noiseRemovalWidget) NoiseRemovalWidget (class in darfix.gui.noiseRemovalWidget) normalize() (in module darfix.core.imageRegistration)

O

Operation (class in darfix.core.dataset)

P

partition_by_intensity() (darfix.core.dataset.Dataset method) pca() (darfix.core.dataset.Dataset method)

PCAWidget (class in darfix.gui.PCAWidget) PlotRockingCurves (class in darfix.gui.displayComponentsWidget)

R

random_search() (in module darfix.core.imageRegistration) remove_dim() (darfix.core.dataset.Dataset method) removeDim() (darfix.gui.dimensionsWidget.DimensionMapping method) resetROI() (darfix.gui.roiSelectionWidget.ROISelectionWidget method)

resetStack() (darfix.gui.roiSelectionWidget.ROISelectionWidget method) reshape() (darfix.core.dataset.Data method) reshape_data() (darfix.core.dataset.Dataset method) ROISelectionWidget (class in darfix.gui.roiSelectionWidget)

S

save() (darfix.core.dataset.Data method) select() (darfix.core.geneticShiftDetection.GeneticShiftDetection method) set_size() (darfix.core.dataset.AcquisitionDims method) set_unique_values() (darfix.core.dataset.Dimension method) setComponents() (darfix.gui.displayComponentsWidget.DisplayComponentsWidget method) setDataset() (darfix.gui.blindSourceSeparationWidget.BSSWidget method) (darfix.gui.dataPartitionWidget.DataPartitionWidget method) (darfix.gui.dimensionsWidget.DimensionWidget method) (darfix.gui.noiseRemovalWidget.NoiseRemovalWidget method) (darfix.gui.PCAWidget.PCAWidget method) (darfix.gui.roiSelectionWidget.ROISelectionWidget method) (darfix.gui.shiftCorrectionWidget.ShiftCorrectionWidget method) setDims() (darfix.gui.dimensionsWidget.DimensionWidget method) setFiles() (darfix.gui.datasetSelectionWidget.FilesSelectionWidget method)

setRoi() (darfix.gui.roiSelectionWidget.ROISelectionWidget method) setStack() (darfix.gui.noiseRemovalWidget.NoiseRemovalWidget method) (darfix.gui.roiSelectionWidget.ROISelectionWidget method) (darfix.gui.shiftCorrectionWidget.ShiftCorrectionWidget method) shape() (darfix.core.dataset.AcquisitionDims property) (darfix.core.dataset.Data property) shift_correction() (in module darfix.core.imageRegistration) shift_detection() (in module darfix.core.imageRegistration) ShiftApproach (class in darfix.core.imageRegistration) ShiftCorrectionWidget (class in darfix.gui.shiftCorrectionWidget) singular_values() (darfix.decomposition.ipca.IPCA property) stop_operation() (darfix.core.dataset.Data method) (darfix.core.dataset.Dataset method) support_() (darfix.core.geneticShiftDetection.GeneticShiftDetection property)

T

take() (darfix.core.dataset.Data method) threshold_removal() (in module darfix.core.imageOperations)

to_dict() (darfix.core.dataset.Dimension method) to_memory() (darfix.core.dataset.Dataset method)