decode package

Subpackages

• decode.evaluation package
  • Submodules
  • decode.evaluation.evaluation module
    • DistanceEvaluation
      • DistanceEvaluation.forward()
    • SMLMEvaluation
      • SMLMEvaluation.alpha_ax
      • SMLMEvaluation.alpha_lat
      • SMLMEvaluation.descriptors
      • SMLMEvaluation.effcy_ax
      • SMLMEvaluation.effcy_lat
      • SMLMEvaluation.effcy_vol
      • SMLMEvaluation.forward()
    • SegmentationEvaluation
      • SegmentationEvaluation.forward()
    • WeightedErrors
      • WeightedErrors.forward()
      • WeightedErrors.plot_error()
      • WeightedErrors.reduction
  • decode.evaluation.match_emittersets module
    • EmitterMatcher
      • EmitterMatcher.forward()
    • GreedyHungarianMatching
      • GreedyHungarianMatching.dist_vol
      • GreedyHungarianMatching.filter()
      • GreedyHungarianMatching.forward()
      • GreedyHungarianMatching.parse()
  • decode.evaluation.metric module
    • efficiency()
    • precision_recall_jaccard()
    • rmse_mad_dist()
  • decode.evaluation.predict_dist module
    • deviation_dist()
    • emitter_deviations()
    • px_pointer_dist()
  • decode.evaluation.utils module
    • MetricMeter
      • MetricMeter.avg
      • MetricMeter.count
      • MetricMeter.hist()
      • MetricMeter.mean
      • MetricMeter.reset()
      • MetricMeter.std
      • MetricMeter.update()
    • kde_sorted()
  • Module contents
• decode.generic package
  • Submodules
  • decode.generic.emitter module
    • CoordinateOnlyEmitter
    • EmitterSet
      • EmitterSet.bg_scr
      • EmitterSet.cat()
      • EmitterSet.chunks()
      • EmitterSet.clone()
      • EmitterSet.data
      • EmitterSet.dim()
      • EmitterSet.eq_attr()
      • EmitterSet.filter_by_sigma()
      • EmitterSet.get_subset_frame()
      • EmitterSet.hist_detection()
      • EmitterSet.load()
      • EmitterSet.meta
      • EmitterSet.phot_scr
      • EmitterSet.populate_crlb()
      • EmitterSet.save()
      • EmitterSet.single_frame
      • EmitterSet.sort_by_frame()
      • EmitterSet.sort_by_frame_()
      • EmitterSet.split_in_frames()
      • EmitterSet.to_dict()
      • EmitterSet.xyz_nm
      • EmitterSet.xyz_px
      • EmitterSet.xyz_scr
      • EmitterSet.xyz_scr_nm
      • EmitterSet.xyz_scr_px
      • EmitterSet.xyz_sig_tot_nm
      • EmitterSet.xyz_sig_weighted_tot_nm
    • EmptyEmitterSet
    • LooseEmitterSet
      • LooseEmitterSet.return_emitterset()
      • LooseEmitterSet.sanity_check()
      • LooseEmitterSet.te
    • RandomEmitterSet
    • at_least_one_dim()
    • same_dim_tensor()
    • same_shape_tensor()
  • decode.generic.process module
    • Identity
      • Identity.forward()
    • ProcessEmitters
      • ProcessEmitters.forward()
    • RemoveOutOfFOV
      • RemoveOutOfFOV.clean_emitter()
      • RemoveOutOfFOV.forward()
  • decode.generic.slicing module
    • ix_split()
    • split_sliceable()
  • decode.generic.test_utils module
    • file_loadable()
    • open_n_hash()
    • same_weights()
    • tens_almeq()
  • Module contents
• decode.neuralfitter package
  • Subpackages
    • decode.neuralfitter.inference package
      • Submodules
      • decode.neuralfitter.inference.inference module
      • decode.neuralfitter.inference.pred_tif module
      • Module contents
    • decode.neuralfitter.models package
      • Submodules
      • decode.neuralfitter.models.model_param module
      • decode.neuralfitter.models.model_speced_impl module
      • decode.neuralfitter.models.unet_param module
      • decode.neuralfitter.models.unet_parts module
      • Module contents
    • decode.neuralfitter.train package
      • Submodules
      • decode.neuralfitter.train.live_engine module
      • decode.neuralfitter.train.random_simulation module
      • Module contents
    • decode.neuralfitter.utils package
      • Submodules
      • decode.neuralfitter.utils.collate module
      • decode.neuralfitter.utils.last_layer_dynamics module
      • decode.neuralfitter.utils.log_train_val_progress module
      • decode.neuralfitter.utils.logger module
      • decode.neuralfitter.utils.padding_calc module
      • decode.neuralfitter.utils.probability module
      • decode.neuralfitter.utils.processing module
      • Module contents
  • Submodules
  • decode.neuralfitter.coord_transform module
    • Offset2Coordinate
      • Offset2Coordinate.forward()
      • Offset2Coordinate.parse()
  • decode.neuralfitter.dataset module
    • InferenceDataset
    • SMLMAPrioriDataset
      • SMLMAPrioriDataset.emitter
      • SMLMAPrioriDataset.sample()
    • SMLMDataset
      • SMLMDataset.return_em
      • SMLMDataset.sanity_check()
    • SMLMLiveDataset
      • SMLMLiveDataset.sample()
      • SMLMLiveDataset.sanity_check()
    • SMLMLiveSampleDataset
    • SMLMStaticDataset
  • decode.neuralfitter.de_bias module
    • UniformizeOffset
      • UniformizeOffset.cdf_get()
      • UniformizeOffset.forward()
      • UniformizeOffset.histedges_equal_n()
      • UniformizeOffset.uniformize()
  • decode.neuralfitter.em_filter module
    • EmitterFilter
      • EmitterFilter.forward()
    • NoEmitterFilter
      • NoEmitterFilter.forward()
    • PhotonFilter
      • PhotonFilter.forward()
    • TarEmitterFilter
      • TarEmitterFilter.forward()
  • decode.neuralfitter.frame_processing module
    • AutoCenterCrop
      • AutoCenterCrop.forward()
    • AutoPad
      • AutoPad.forward()
    • FrameProcessing
      • FrameProcessing.forward()
    • Mirror2D
      • Mirror2D.forward()
    • get_frame_extent()
  • decode.neuralfitter.losscollection module
  • decode.neuralfitter.post_processing module
    • ConsistencyPostprocessing
      • ConsistencyPostprocessing.forward()
      • ConsistencyPostprocessing.parse()
      • ConsistencyPostprocessing.sanity_check()
      • ConsistencyPostprocessing.skip_if()
    • LookUpPostProcessing
      • LookUpPostProcessing.forward()
    • NoPostProcessing
      • NoPostProcessing.forward()
    • PostProcessing
      • PostProcessing.forward()
      • PostProcessing.sanity_check()
      • PostProcessing.skip_if()
    • SpatialIntegration
      • SpatialIntegration.forward()
      • SpatialIntegration.set_p_aggregation()
  • decode.neuralfitter.sampling module
    • sample_crop()
  • decode.neuralfitter.scale_transform module
    • AmplitudeRescale
      • AmplitudeRescale.forward()
      • AmplitudeRescale.parse()
    • FourFoldInverseOffsetRescale
      • FourFoldInverseOffsetRescale.forward()
    • InverseOffsetRescale
      • InverseOffsetRescale.forward()
      • InverseOffsetRescale.parse()
    • InverseParamListRescale
      • InverseParamListRescale.forward()
    • OffsetRescale
      • OffsetRescale.forward()
      • OffsetRescale.parse()
      • OffsetRescale.return_inverse()
    • ParameterListRescale
      • ParameterListRescale.forward()
      • ParameterListRescale.parse()
    • SpatialInterpolation
      • SpatialInterpolation.forward()
  • decode.neuralfitter.target_generator module
    • DisableAttributes
      • DisableAttributes.forward()
      • DisableAttributes.parse()
    • FourFoldEmbedding
      • FourFoldEmbedding.forward()
      • FourFoldEmbedding.parse()
    • ParameterListTarget
      • ParameterListTarget.forward()
    • TargetGenerator
      • TargetGenerator.forward()
      • TargetGenerator.sanity_check()
    • UnifiedEmbeddingTarget
      • UnifiedEmbeddingTarget.const_roi_target()
      • UnifiedEmbeddingTarget.forward()
      • UnifiedEmbeddingTarget.forward_()
      • UnifiedEmbeddingTarget.parse()
      • UnifiedEmbeddingTarget.single_px_target()
      • UnifiedEmbeddingTarget.xextent
      • UnifiedEmbeddingTarget.xy_target()
      • UnifiedEmbeddingTarget.yextent
  • decode.neuralfitter.train_val_impl module
    • ship_device()
    • test()
    • train()
  • decode.neuralfitter.weight_generator module
    • FourFoldSimpleWeight
      • FourFoldSimpleWeight.forward()
      • FourFoldSimpleWeight.parse()
    • SimpleWeight
      • SimpleWeight.check_forward_sanity()
      • SimpleWeight.check_sanity()
      • SimpleWeight.forward()
      • SimpleWeight.parse()
    • WeightGenerator
      • WeightGenerator.check_forward_sanity()
      • WeightGenerator.forward()
      • WeightGenerator.parse()
  • Module contents
• decode.plot package
  • Submodules
  • decode.plot.fancy_plot module
    • plot_crosshair()
  • decode.plot.frame_coord module
    • PlotCoordinates
      • PlotCoordinates.plot()
    • PlotCoordinates3D
      • PlotCoordinates3D.plot()
    • PlotFrame
      • PlotFrame.plot()
    • PlotFrameCoord
      • PlotFrameCoord.plot()
    • connect_point_set()
  • Module contents
• decode.renderer package
  • Submodules
  • decode.renderer.renderer module
    • Renderer
      • Renderer.forward()
      • Renderer.render()
    • Renderer2D
      • Renderer2D.forward()
      • Renderer2D.get_extent()
      • Renderer2D.render()
    • RendererIndividual2D
      • RendererIndividual2D.calc_gaussians()
  • Module contents
• decode.simulation package
  • Submodules
  • decode.simulation.background module
    • Background
      • Background.forward()
      • Background.sample()
      • Background.sample_like()
      • Background.sanity_check()
    • BgPerEmitterFromBgFrame
      • BgPerEmitterFromBgFrame.forward()
    • UniformBackground
      • UniformBackground.parse()
      • UniformBackground.sample()
  • decode.simulation.camera module
    • Camera
      • Camera.backward()
      • Camera.forward()
    • PerfectCamera
      • PerfectCamera.parse()
    • Photon2Camera
      • Photon2Camera.backward()
      • Photon2Camera.forward()
      • Photon2Camera.parse()
    • SCMOS
      • SCMOS.check_sanity()
      • SCMOS.forward()
      • SCMOS.forward_on_sampled_sensor_window()
      • SCMOS.sample_sensor_window()
  • decode.simulation.emitter_generator module
    • EmitterPopperMultiFrame
    • EmitterPopperSingle
    • EmitterSampler
      • EmitterSampler.sample()
    • EmitterSamplerBlinking
      • EmitterSamplerBlinking.num_frames
      • EmitterSamplerBlinking.parse()
      • EmitterSamplerBlinking.sample()
      • EmitterSamplerBlinking.sample_loose_emitter()
      • EmitterSamplerBlinking.sample_n()
      • EmitterSamplerBlinking.t0_dist
    • EmitterSamplerFrameIndependent
      • EmitterSamplerFrameIndependent.em_avg
      • EmitterSamplerFrameIndependent.photon_range
      • EmitterSamplerFrameIndependent.sample()
      • EmitterSamplerFrameIndependent.sample_n()
  • decode.simulation.noise_distributions module
    • Gamma
      • Gamma.forward()
    • Gaussian
      • Gaussian.forward()
    • NoiseDistribution
      • NoiseDistribution.forward()
    • Poisson
      • Poisson.forward()
    • ZeroNoise
      • ZeroNoise.forward()
  • decode.simulation.psf_kernel module
    • CubicSplinePSF
      • CubicSplinePSF.coord2impl()
      • CubicSplinePSF.cpu()
      • CubicSplinePSF.crlb()
      • CubicSplinePSF.crlb_sq()
      • CubicSplinePSF.cuda()
      • CubicSplinePSF.cuda_compiled
      • CubicSplinePSF.cuda_is_available()
      • CubicSplinePSF.derivative()
      • CubicSplinePSF.fisher()
      • CubicSplinePSF.forward()
      • CubicSplinePSF.forward_rois()
      • CubicSplinePSF.frame2roi_coord()
      • CubicSplinePSF.inv_default()
      • CubicSplinePSF.n_par
      • CubicSplinePSF.sanity_check()
    • DeltaPSF
      • DeltaPSF.bin_ctr_x
      • DeltaPSF.bin_ctr_y
      • DeltaPSF.forward()
      • DeltaPSF.search_bin_index()
    • GaussianPSF
      • GaussianPSF.astigmatism()
      • GaussianPSF.forward()
    • PSF
      • PSF.crlb()
      • PSF.forward()
  • decode.simulation.simulator module
    • Simulation
      • Simulation.forward()
      • Simulation.sample()
  • decode.simulation.structure_prior module
    • RandomStructure
      • RandomStructure.area
      • RandomStructure.parse()
      • RandomStructure.sample()
    • StructurePrior
      • StructurePrior.area
      • StructurePrior.sample()
  • Module contents
• decode.utils package
  • Submodules
  • decode.utils.bookkeeping module
    • decode_state()
  • decode.utils.calibration_io module
    • SMAPSplineCoefficient
      • SMAPSplineCoefficient.init_spline()
  • decode.utils.checkpoint module
    • CheckPoint
      • CheckPoint.dict
      • CheckPoint.dump()
      • CheckPoint.load()
      • CheckPoint.save()
      • CheckPoint.update()
  • decode.utils.emitter_io module
    • EmitterWriteStream
      • EmitterWriteStream.write()
    • get_decode_meta()
    • load_csv()
    • load_h5()
    • load_smap()
    • load_torch()
    • save_csv()
    • save_h5()
    • save_torch()
  • decode.utils.emitter_trafo module
    • transform_emitter()
  • decode.utils.example_helper module
    • load_example_package()
    • load_gateway()
  • decode.utils.frames_io module
    • BatchFileLoader
      • BatchFileLoader.remove_by_exclude()
    • TiffTensor
    • load_tif()
  • decode.utils.loader module
    • check_file()
    • check_load()
    • load()
  • decode.utils.model_io module
    • LoadSaveModel
      • LoadSaveModel.load_init()
      • LoadSaveModel.save()
    • hash_model()
  • decode.utils.notebooks module
    • copy_pkg_file()
    • load_examples()
    • parse_args()
  • decode.utils.param_io module
    • ParamHandling
      • ParamHandling.convert_param_debug()
      • ParamHandling.convert_param_file()
      • ParamHandling.file_extensions
      • ParamHandling.load_params()
      • ParamHandling.write_params()
    • add_root_relative()
    • autofill_dict()
    • autoset_scaling()
    • copy_reference_param()
    • load_params()
    • load_reference()
    • save_params()
  • decode.utils.types module
    • RecursiveNamespace
      • RecursiveNamespace.keys()
      • RecursiveNamespace.map_entry()
      • RecursiveNamespace.to_dict()
  • Module contents

Module contents

DECODE This software package implements a DeepLearning based framework for high-density fitting in SMLM.