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.gitignore
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# append all sym links to .gitignore file, needs to be run from repository folder
# find . -type l | sed -e s'/^\.\///g' >> .gitignore
*.suc
*.aux
*.djs
*.synctex.gz
*.sym
*.syc
*.sub
*.pdf
*.acr
*.bbl
*.blg
*.idx
*.mw
DYNAMO_INITIALIZED
CONFIGURATION
matlab_shell.sh
run_TomoBEAR.sh
TomoBEAR.prj
tomoBEAR/
TomoBEAR/
test
load_modules.sh
SUSAN_new/
SUSAN/
SUSAN_old/
extern
extern/semaphore/
extern/CTFcorrection_v1_2/
test_cry/
.currentCtffind.dff
.etomologs
etomo_*
data
sqlite
job_data
*.m~
*.M~
*.json~
*.sh~
*.asv
**/.vscode
*.mexw64
*.mexmaci64
*.mexa64
**/temp
**/tmp
temporary
tests
codegen
*.pyc
**/__pycache__
*.st
*.em
*.mrc
*.mrcs
*.tif
*.ali
*.preali
*.rec
*.png
*.jpg
*.gif
*.coverage
*.e*
*.o*
tomoBEAR
playgorund/
nn/
offxca/
*.mldatx
*.log
combine_configurations_and_save_history
cryo_et_pipeline
cryo_et_pipeline_local
#cryo_et_pipeline.prj
*.sbatch~
*~
**/node_modules
web/javascript/backend/node_modules
web/javascript/frontend/node_modules
.idea
.vscode
*.suo
*.ntvs*
*.njsproj
*.sln
*.sw?
slurm-*.out
bfg-report/
matlab_shell.sh
run_tomoBEAR.sh
run_TomoBEAR.sh
dynamo/matlab/src/dynamo_table_rescale.m
dynamo/matlab/src/+dpkproject/recomputeCC.m
dynamo/matlab/mbtools/+mbparse/@output
dynamo/matlab/src/+dpksys
dynamo/matlab/src/dynamo_read_subtomogram.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepWrapper/compute.m
dynamo/matlab/src/+dpkproject/readNextIterationFile.m
dynamo/matlab/src/+dpkproject/writeNextIterationFile.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@FullStatusManager/assessWorkflowInput.m
dynamo/matlab/src/+dpktilt/+aux/+align/+pipeline/+steps/+restorers/@MarkerRestorer/takeSnapshotInput.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepRestorer/setSnapshotInput.m
dynamo/matlab/src/+dpktilt/+aux/+align/+pipeline/+steps/+restorers/@MarkerRestorer/takeSnapshotOutput.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepRestorer/setSnapshotOutput.m
dynamo/matlab/mbtools/+mbgui/+dlg/@msgbox/msgbox.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepManager/reload.m
dynamo/matlab/mbtools/+mboop/+listener/timebomb.m
dynamo/matlab/mbtools/+mbparse/+files/+absolutePath/getAbsolutePath.m
dynamo/matlab/src/+dpktilt/+aux/+align/+fitters/+aux/@Status/conditionalUpdateFitter.m
dynamo/matlab/src/+dpktilt/+aux/+align/+fitters/+aux/@Status/conditionalUpdateResiduals.m
dynamo/matlab/src/+dpktilt/+aux/+align/+pipeline/+usr/@Enter/detectionBinningFactor.m
dynamo/matlab/src/+dpktilt/+aux/+tsa/+parsing/loadOldWorkflow.m
dynamo/matlab/src/@dBoxes/assertData.m
dynamo/matlab/src/@dBoxes/convertSimpleData.m
dynamo/matlab/src/@dBoxes/enterParticle.m
dynamo/matlab/src/@dBoxes/getParticleFile.m
dynamo/matlab/src/@dBoxes/setMetadata.m
dynamo/matlab/src/@dBoxes/setup.m
dynamo/matlab/src/@dMetadata/dMetadata.m
dynamo/matlab/src/dynamo__fsc_get_resolution.m
dynamo/matlab/src/dynamo_compare_fsc.m
dynamo/matlab/src/dynamo_compare_plots.m
dynamo/matlab/src/dynamo_copyfile.m
dynamo/matlab/src/dynamo_fsc.m
dynamo/matlab/src/dynamo_read_sel.m
dynamo/matlab/src/dynamo_read_src.m
dynamo/matlab/src/dynamo_table_eo.m
dynamo/matlab/src/dynamo_tag2file.m
dynamo/matlab/src/dynamo_vpr_eo.m
dynamo/matlab/src/dynamo_write_src.m
dynamo/matlab/src/dynamo_zaux_multisymbol.m
dynamo/matlab/src/shorthands/dfsc.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/
dynamo/matlab/src/column_checkin.m
dynamo/matlab/src/dynamo__parse_str2numall.m
dynamo/matlab/src/dynamo__rigid_order.m
dynamo/matlab/src/dynamo_file_checkin.m
dynamo/matlab/src/dynamo_fsampling_symmetrize.m
dynamo/matlab/src/dynamo_montage.m
dynamo/matlab/src/dynamo_montage_no_license.m
dynamo/matlab/src/dynamo_rigid_compare.m
dynamo/matlab/src/dynamo_rigid_force.m
dynamo/matlab/src/dynamo_rot_solid.m
dynamo/matlab/src/dynamo_table_compare.m
dynamo/matlab/src/dynamo_tags_in_table.m
dynamo/matlab/src/maprange.m
dynamo/matlab/src/shorthands/dnan.m
dynamo/matlab/src/+dpkvol/@Volume/extractBlock.m
dynamo/matlab/src/dynamo_extract_slices.m
dynamo/matlab/src/dynamo__show.m
dynamo/matlab/src/dynamo_cellcube.m
dynamo/matlab/src/dynamo__regexp2files_ifregexp.m
dynamo/matlab/src/dynamo__color2rgb.m
dynamo/matlab/src/dynamo_slices.m
dynamo/matlab/src/dynamo_tag2ptable.m
dynamo/matlab/src/dispc.m
dynamo/matlab/src/row_checkin.m
dynamo/matlab/src/dynamo_aux_resolution_label.m
dynamo/matlab/src/dynamo_fsc_fouriermask.m
dynamo/matlab/src/num_checkin.m
dynamo/matlab/src/dynamo_particle.m
dynamo/matlab/src/dynamo_nan.m
dynamo/matlab/src/dynamo_fweight_divide.m
dynamo/matlab/src/+dpkgeom/+rotation/sharpShiftRot.m
dynamo/matlab/src/dynamo_tag2particle.m
dynamo/matlab/src/dynamo__action_chain_parse.m
dynamo/matlab/src/dynamo__query_checkout_as_folder.m
dynamo/matlab/src/@dData/setMetadata.m
dynamo/matlab/src/@dData/new.m
dynamo/matlab/src/@dData/getReferencedTags.m
dynamo/matlab/src/dynamo_table_import.m
dynamo/matlab/src/+ptdb/query2tomogram_ifquery.m
dynamo/matlab/src/shorthands/daverage.m
dynamo/matlab/src/dynamo_average.m
dynamo/matlab/src/dynamo__flag_read.m
dynamo/matlab/src/dynamo__parse_sym.m
dynamo/matlab/src/dynamo__parameter.m
dynamo/matlab/src/dynamo_rigid_compose.m
dynamo/matlab/src/dynamo_rigid.m
dynamo/matlab/src/+dpkproject/addPtable.m
dynamo/matlab/src/+dpkproject/+pipeline/genericInput2Average.m
dynamo/matlab/src/+dpkproject/adaptiveBandapassEOreunfold.m
dynamo/matlab/src/dynamo_vpr_info_convergence.m
dynamo/matlab/src/dynamo_filename_prepend.m
dynamo/matlab/src/dynamo_pipeline_CC_intermediate_average.m
dynamo/matlab/src/+dpkproject/+pipeline/average.m
dynamo/matlab/src/+dpkproject/adaptiveFiltering.m
dynamo/matlab/src/+dpkproject/+pipeline/isAverageNeeded.m
dynamo/matlab/src/dynamo_database_write.m
dynamo/matlab/src/dynamo_table_marktag.m
dynamo/matlab/src/dynamo_pipeline_threshold.m
dynamo/matlab/src/+dpkproject/+parameters/getFromIte.m
dynamo/matlab/src/+dpkproject/+pipeline/overlappingParticles.m
dynamo/matlab/src/+dpkproject/assemble_checkPeak.m
dynamo/matlab/src/+dpkproject/+pipeline/+tables/gatherGPUforIteRef.m
dynamo/matlab/src/dynamo_zaux_rescalings.m
dynamo/matlab/src/+dpkproject/gatherTablesAfterProcess.m
dynamo/matlab/src/dynamo_cc.m
dynamo/matlab/src/dynamo_ccmatrix_assemble.m
dynamo/matlab/src/dynamo_ccmatrix_compute.m
dynamo/matlab/src/dynamo_iteration_check.m
dynamo/matlab/src/+dpkproject/+plugins/+post/getCommands.m
dynamo/matlab/src/dynamo_plugin_post_multireference_tutorial.m
dynamo/matlab/src/dynamo_iteration_assemble.m
dynamo/matlab/src/dynamo_pipeline_system_check_output_gpu.m
dynamo/matlab/src/dynamo_card_write_in.m
dynamo/matlab/src/@dDataOld/assertData.m
dynamo/matlab/src/@dDataOld/getParticleFile.m
dynamo/matlab/src/+dpkdata/+aux/facts2dData.m
dynamo/matlab/src/+dpkproject/+pipeline/+gpu/createParticleFileListAssignations.m
dynamo/matlab/src/dynamo_guitool_information.m
dynamo/matlab/src/dynamo_sphere.m
dynamo/matlab/src/dynamo_resize_mask.m
dynamo/matlab/src/dynamo_pipeline_resize.m
dynamo/matlab/src/dynamo_database_volume_process.m
dynamo/matlab/src/+dpkproject/preprocessReferences.m
dynamo/matlab/src/dynamo_tags_write.m
dynamo/matlab/src/+dpkproject/setupFreezingShifts.m
dynamo/matlab/src/+dpkproject/setup_freezing_angular_references.m
dynamo/matlab/src/dynamo_aux_appendlog.m
dynamo/matlab/src/+dpkproject/+pipeline/setSurvivingReferences.m
dynamo/matlab/src/+dpkproject/+pipeline/getSurvivingReferences.m
dynamo/matlab/src/dynamo_card_read.m
dynamo/matlab/src/dynamo_iteration_setup.m
dynamo/matlab/src/+dpkproject/+progress/readCompletedGPUTasks.m
dynamo/matlab/src/dynamo_database_read.m
dynamo/matlab/src/dynamo__end_iteration.m
dynamo/matlab/src/dynamo_filename_regexp2realfiles.m
dynamo/matlab/src/dynamo__last_completed_iteration.m
dynamo/matlab/src/dynamo_project_progress.m
dynamo/matlab/src/+pparse/isregexp.m
dynamo/cuda/bin/dynamo_compute_iteration_spp
dynamo/matlab/src/dynamo_vpr_status.m
dynamo/matlab/dynamo_compute_iteration_spp
dynamo/matlab/src/dynamo__query_gettable.m
dynamo/matlab/src/+dpkproject/+parse/projectLocation.m
dynamo/matlab/src/dynamo__query_convention.m
dynamo/matlab/src/dynamo__query2elements.m
dynamo/matlab/src/dynamo_db.m
dynamo/matlab/src/shorthands/ddb.m
dynamo/matlab/src/+dpkproject/+runtime/getGPUmotor.m
dynamo/matlab/mbtools/src/+mbgpu/+check/deviceNumber.m
dynamo/matlab/src/+dpkproject/+runtime/+checks/gpu.m
dynamo/matlab/src/dynamo_execute_project.m
dynamo/matlab/src/dynamo_vpr_run.m
dynamo/matlab/src/shorthands/dvrun.m
dynamo/matlab/src/+dpkproject/executionScript.m
dynamo/matlab/src/+dpkproject/+executionScript/createForMatlab.m
dynamo/matlab/src/dynamo_vpr_execution_script.m
dynamo/matlab/src/dynamo_zaux_card_order.m
dynamo/matlab/src/dynamo_card_write.m
dynamo/matlab/src/dynamo_intertwin_ite2round.m
dynamo/matlab/src/dynamo_pipeline_setup_card_ite.m
dynamo/matlab/src/dynamo_zaux_intertwin_round_identifier_array.m
dynamo/matlab/src/dynamo_pipeline_settings2first_references.m
dynamo/matlab/src/dynamo_pipeline_links2settings.m
dynamo/matlab/src/+dpkproject/templateAndDataFeatures.m
dynamo/matlab/src/+dpkproject/unfoldCheckAdaptiveBandpassInitial.m
dynamo/matlab/src/+pparse/varargin_catch_project_parameters.m
dynamo/matlab/src/dynamo_vpr_unfold.m
dynamo/matlab/src/shorthands/dvunfold.m
dynamo/matlab/src/dynamo_find_root.m
dynamo/matlab/src/dynamo_database_linked_file_read.m
dynamo/matlab/src/dynamo_check_initial_folders.m
dynamo/matlab/src/dynamo_isdata.m
dynamo/matlab/src/dynamo_whatis.m
dynamo/matlab/src/dynamo_vpr_statistics.m
dynamo/matlab/src/dynamo_vpr_check.m
dynamo/matlab/src/shorthands/dvcheck.m
dynamo/matlab/src/dynamo_filename_change_extension.m
dynamo/matlab/src/dynamo_doc_append.m
dynamo/matlab/src/dynamo_copyfile.m
dynamo/matlab/src/shorthands/dwrite_multireference.m
dynamo/matlab/src/dynamo_parameter.m
dynamo/matlab/src/dynamo__shortform2form_ifshortform.m
dynamo/matlab/src/dynamo__system_parse_char_arguments_EVEN.m
dynamo/matlab/src/+dpkproject/+vpr/addMissingConventionParameters.m
dynamo/matlab/src/dynamo_vpr_load.m
dynamo/matlab/src/dynamo__vprf_inputfile.m
dynamo/matlab/src/dynamo__bdl2cell_ifbdl.m
dynamo/matlab/src/dynamo__parse_bar2cell_ifbar.m
dynamo/matlab/src/dynamo_vpr_put.m
dynamo/matlab/src/shorthands/dvput.m
dynamo/matlab/src/dvput.m
dynamo/matlab/src/dynamo__format_item.m
dynamo/matlab/src/dynamo__doc2cell_ifdoc.m
dynamo/matlab/src/dynamo__sel2cell_ifsel.m
dynamo/matlab/src/dynamo_write_multireference.m
dynamo/matlab/src/dynamo_vpr_multireference_setfiles.m
dynamo/matlab/src/+pparse/filenameCompact.m
dynamo/matlab/src/dynamo_vpr_absolute_path.m
dynamo/matlab/src/dynamo_vpr_hint_files.m
dynamo/matlab/src/dynamo__vpr_modify_round2all.m
dynamo/matlab/src/dynamo__varargin.m
dynamo/matlab/src/dynamo_vpr_modify.m
dynamo/matlab/src/dynamo_filename_mkdir.m
dynamo/matlab/src/dynamo_vpr_correct_defaults.m
dynamo/matlab/src/structcell_checkout.m
dynamo/matlab/src/dynamo_database_parse.m
dynamo/matlab/src/dynamo_database_convention.m
dynamo/matlab/src/dynamo_database_locate.m
dynamo/matlab/src/dynamo__varargin_catch_round_parameters.m
dynamo/matlab/src/dynamo_vpr_convention.m
dynamo/matlab/src/dynamo__varargin_catch_project_parameters.m
dynamo/matlab/src/dynamo_vpr.m
dynamo/matlab/src/dynamo_vpr_save.m
dynamo/matlab/src/+dpkproject/+parsers/@ParserSeeds/ParserSeeds.m
dynamo/matlab/src/@dcp/dcp.m
dynamo/matlab/src/@dcp/new.m
dynamo/matlab/src/+dpktilt/+aux/+align/+pipeline/+usr/@Enter/detectionBinningFactor.m
dynamo/matlab/src/+dpktilt/+aux/+align/+fitters/+aux/@Status/conditionalUpdateFitter.m
dynamo/matlab/mbtools/+mboop/+listener/timebomb.m
dynamo/matlab/mbtools/+mbgui/+dlg/@msgbox/msgbox.m
dynamo/matlab/mbtools/+mbs/oh.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepManager/reload.m
dynamo/matlab/src/+dpktilt/+aux/+align/+fitters/+aux/@Status/conditionalUpdateResiduals.m
dynamo/matlab/mbtools/+mbparse/+files/+absolutePath/getAbsolutePath.m
dynamo/matlab/src/+dpktilt/+aux/+tsa/+parsing/loadOldWorkflow.m
dynamo/matlab/mbtools/+mbg/+aux/+mbtable/@Grep/Grep.m
dynamo/matlab/mbtools/+mbg/+aux/+mbtable/@IO/IO.m
dynamo/matlab/mbtools/+mbg/+aux/+mbtable/@IO/infereRowFormat.m
dynamo/matlab/mbtools/+mbg/+aux/+mbtable/@IO/tableContents2FidAsText.m
dynamo/matlab/mbtools/+mbg/+aux/+mbtable/@RowExtractor/RowExtractor.m
dynamo/matlab/mbtools/+mbg/cellCheckin.m
dynamo/matlab/mbtools/+mbg/cellCheckout.m
dynamo/matlab/mbtools/+mbg/cellCompact.m
dynamo/matlab/mbtools/+mbg/cellStretch.m
dynamo/matlab/mbtools/+mbg/dispv.m
dynamo/matlab/mbtools/+mbg/isemptyCellContents.m
dynamo/matlab/mbtools/+mbg/setDefault.m
dynamo/matlab/mbtools/+mbgeom/+coords/@SubvolumeRescale/SubvolumeRescale.m
dynamo/matlab/mbtools/+mbgeom/+coords/@SubvolumeRescale/configure.m
dynamo/matlab/mbtools/+mbgeom/+coords/@SubvolumeRescale/setCanvasLowest.m
dynamo/matlab/mbtools/+mbgeom/+coords/@SubvolumeRescale/setCanvasUppest.m
dynamo/matlab/mbtools/+mbgeom/+coords/@SubvolumeRescale/setChunkLowest.m
dynamo/matlab/mbtools/+mbgeom/+coords/@SubvolumeRescale/setChunkUppest.m
dynamo/matlab/mbtools/+mbgeom/+distances/+cloudshift/@MatchPlotter/MatchPlotter.m
dynamo/matlab/mbtools/+mbgeom/+distances/+cloudshift/@Matcher/Matcher.m
dynamo/matlab/mbtools/+mbgeom/+distances/+cloudshift/@Matcher/computeByBinning.m
dynamo/matlab/mbtools/+mbgeom/+distances/cloud2cloud2D.m
dynamo/matlab/mbtools/+mbgeom/+partition/+tileTypes/@BinnedTile/BinnedTile.m
dynamo/matlab/mbtools/+mbgeom/+partition/+tileTypes/@BinnedTile/setRanges.m
dynamo/matlab/mbtools/+mbgeom/+partition/+tileTypes/@DerivedTile/DerivedTile.m
dynamo/matlab/mbtools/+mbgeom/+partition/@GridPartition/GridPartition.m
dynamo/matlab/mbtools/+mbgeom/+partition/@GridPartition/createTiles.m
dynamo/matlab/mbtools/+mbgeom/+partition/@GridTile/GridTile.m
dynamo/matlab/mbtools/+mbgeom/+partition/@Partition/Partition.m
dynamo/matlab/mbtools/+mbgeom/+partition/@Tile/Tile.m
dynamo/matlab/mbtools/+mbgeom/+partition/@Tile/prettyRange.m
dynamo/matlab/mbtools/+mbgeom/+sets/findAny.m
dynamo/matlab/mbtools/+mbgeom/circle.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/+events/@Change/Change.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/+events/@MultiRemove/MultiRemove.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@Grep/Grep.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@IO/IO.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@IO/infoLines.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@ShapeEvent/ShapeEvent.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@VideoGrep/VideoGrep.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@VideoGrep/dynamicMinimumOccupancy.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@VideoGrep/getTrimmer.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@VideoGrep/inAtLeastNFrames.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@VideoGrep/shapesPerFrame.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+aux/@VideoMath/VideoMath.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+menus/@MenuOptions/MenuOptions.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+plotManagers/@ForPointTrackGroup/ForPointTrackGroup.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+shapeTypes/@VideoTrack/VideoTrack.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+videoTypes/+points/@PointTrack/PointTrack.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+videoTypes/+points/@PointTrack/getIndexedCloud.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/+videoTypes/+points/@PointTrack/setIndexedCloud.m
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dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/@Shape/Shape.m
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dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/@ShapeSet/clone.m
dynamo/matlab/mbtools/+mbgraph/+annotations/+shapeSets/@ShapeSet/notifyCoordinateChange.m
dynamo/matlab/mbtools/+mbgraph/delete.m
dynamo/matlab/mbtools/+mbgui/+menus/@MenuOptionsLibrary/MenuOptionsLibrary.m
dynamo/matlab/mbtools/+mbimg/+embed/embedInMask.m
dynamo/matlab/mbtools/+mbimg/+match/+copies/rosemanCorrelationMatrix.m
dynamo/matlab/mbtools/+mbimg/+match/rosemanLocal.m
dynamo/matlab/mbtools/+mbimg/+transform/+library/@TransformList/TransformList.m
dynamo/matlab/mbtools/+mbimg/binarize.m
dynamo/matlab/mbtools/+mbimg/normalize.m
dynamo/matlab/mbtools/+mbimg/peaks.m
dynamo/matlab/mbtools/+mbio/+aux/+getFilename/+cells/transferableFolder.m
dynamo/matlab/mbtools/+mbio/+readas/textlines.m
dynamo/matlab/mbtools/+mbio/+writeas/textlines.m
dynamo/matlab/mbtools/+mbio/@AccessManager/AccessManager.m
dynamo/matlab/mbtools/+mbio/@AccessManager/isfile.m
dynamo/matlab/mbtools/+mbio/@FileLocation/FileLocation.m
dynamo/matlab/mbtools/+mbio/@FileLocation/getFilename.m
dynamo/matlab/mbtools/+mbio/@FileLocation/setFilename.m
dynamo/matlab/mbtools/+mbio/fopen.m
dynamo/matlab/mbtools/+mbio/getFilename.m
dynamo/matlab/mbtools/+mbio/isfile.m
dynamo/matlab/mbtools/+mbio/isfolder.m
dynamo/matlab/mbtools/+mbio/read.m
dynamo/matlab/mbtools/+mbmath/+peaks2d/robustPeaks.m
dynamo/matlab/mbtools/+mbmath/+peaks2d/subpixelSpline.m
dynamo/matlab/mbtools/+mbmath/+sets/replace.m
dynamo/matlab/mbtools/+mbmath/norm.m
dynamo/matlab/mbtools/+mboop/+container/@Map/Map.m
dynamo/matlab/mbtools/+mboop/+events/@ChangedValue/ChangedValue.m
dynamo/matlab/mbtools/+mboop/+events/@genericData/genericData.m
dynamo/matlab/mbtools/+mboop/+fhc/@PathProvider/PathProvider.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/+areas/@AreaManager/AreaManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/+libraries/@Library/Library.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/+libraries/@Library/executeSteps.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/+libraries/@Library/linkToWorkflow.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/+libraries/@Library/registerDataGate.m
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dynamo/matlab/mbtools/+mboop/+flows/+aux/@ContentManager/ContentManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ContentManager/addLibrary.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@FullStatusManager/FullStatusManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@FullStatusManager/evaluate.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@HeadlessnessSwitch/HeadlessnessSwitch.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@HeadlessnessSwitch/oh.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@IOManager/IOManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@IOManager/subsref.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@InputLinkerManager/InputLinkerManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/ParameterManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/addParameterKey.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/configureActionAfterUpdate.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/fromAreas.m
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dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/getCell.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/getStandardLocation.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/linesForWorkflowConfigurationFile.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/processTextLineAsParameterInput.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/qualifiedNames.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/synchronize.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/writeFile.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@ParameterManager/writeStandardLocation.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@SettingsManager/SettingsManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@SettingsManager/addAreaComputing.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@SettingsManager/addAreaGeneral.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepIdentifier/StepIdentifier.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepLoader/StepLoader.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepManager/StepManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepManager/addStep.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepManager/executeStepList.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepManager/getCell.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepParametersManager/StepParametersManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepParametersManager/addParameter.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepPostProcess/StepPostProcess.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepPostProcess/standardSaveResults.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepRestorer/StepRestorer.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepScannerManager/StepScannerManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/StepStatusManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/addInputItem.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/addItem.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/addOutputItem.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/evaluate.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/lookoutConfiguration.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepStatusManager/setInputFromStepOutput.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepViewerManager/StepViewerManager.m
dynamo/matlab/mbtools/+mboop/+flows/+aux/@StepWrapper/StepWrapper.m
dynamo/matlab/mbtools/+mboop/+flows/+stepTypes/@DynamicStep/DynamicStep.m
dynamo/matlab/mbtools/+mboop/+flows/@DeveloperOptions/DeveloperOptions.m
dynamo/matlab/mbtools/+mboop/+flows/@Step/Step.m
dynamo/matlab/mbtools/+mboop/+flows/@Step/addParameter.m
dynamo/matlab/mbtools/+mboop/+flows/@Step/locateLibraries.m
dynamo/matlab/mbtools/+mboop/+flows/@Viewer/Viewer.m
dynamo/matlab/mbtools/+mboop/+functions/@FunctionHandle/FunctionHandle.m
dynamo/matlab/mbtools/+mboop/+functions/isFunction.m
dynamo/matlab/mbtools/+mboop/+handles/@DynamicProps/DynamicProps.m
dynamo/matlab/mbtools/+mboop/+handles/@DynamicProps/assignprop.m
dynamo/matlab/mbtools/+mboop/+handles/@LocationCoupledToName/LocationCoupledToName.m
dynamo/matlab/mbtools/+mboop/+handles/@Transferable/Transferable.m
dynamo/matlab/mbtools/+mboop/+handles/@silent/silent.m
dynamo/matlab/mbtools/+mboop/+identity/@Credentials/Credentials.m
dynamo/matlab/mbtools/+mboop/+identity/@Credentials/addComment.m
dynamo/matlab/mbtools/+mboop/+listener/bindLifeCycle.m
dynamo/matlab/mbtools/+mboop/+namespaces/@functionality/functionality.m
dynamo/matlab/mbtools/+mboop/@handle/cloneof.m
dynamo/matlab/mbtools/+mboop/@handle/copyContents.m
dynamo/matlab/mbtools/+mboop/@handle/copyof.m
dynamo/matlab/mbtools/+mboop/@handle/handle.m
dynamo/matlab/mbtools/+mboop/@handleDisk/getCurrentAbsoluteLocationInDisk.m
dynamo/matlab/mbtools/+mboop/@handleDisk/getLocationInDisk.m
dynamo/matlab/mbtools/+mboop/@handleDisk/handleDisk.m
dynamo/matlab/mbtools/+mboop/@simpleflow/configureSettings.m
dynamo/matlab/mbtools/+mboop/@simpleflow/getConfigurationTextFile.m
dynamo/matlab/mbtools/+mboop/@simpleflow/shg.m
dynamo/matlab/mbtools/+mboop/@simpleflow/simpleflow.m
dynamo/matlab/mbtools/+mboop/addElement.m
dynamo/matlab/mbtools/+mboop/findIndex.m
dynamo/matlab/mbtools/+mboop/ismember.m
dynamo/matlab/mbtools/+mboop/unique.m
dynamo/matlab/mbtools/+mbp/+datagate/+MI/@ContainsLinkable/ContainsLinkable.m
dynamo/matlab/mbtools/+mbp/+datagate/+MI/@ContainsLinkable/createLinkedGates.m
dynamo/matlab/mbtools/+mbp/+datagate/+MI/@ContainsLinkable/provideLinkedGates.m
dynamo/matlab/mbtools/+mbp/+datagate/+identity/@Credentials/Credentials.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@IndexedCloud/IndexedCloud.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@IndexedCloud/configureClassMenuCallbacks.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@IndexedCloud/viewerTracesOnVideo.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@IndexedCloud/viewerTracesSimplePlot.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@ShapeSet/ShapeSet.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@ShapeSet/configureClassMenuCallbacks.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@ShapeSet/viewerOccupancy.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/Stack.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/configureClassMenuCallbacks.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/getCenter2D.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/getNumberFrames.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/getSize.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/viewer3dmod.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/viewerInfo.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/viewerTomoshowMemory.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/+lib/@Stack/viewerTomoshowOnTheFly.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/@Inspector/Inspector.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/@Inspector/configureClassMenuCallbacks.m
dynamo/matlab/mbtools/+mbp/+datagate/+inspectors/@Inspector/connectViewerList.m
dynamo/matlab/mbtools/+mbp/+datagate/@DataGate/DataGate.m
dynamo/matlab/mbtools/+mbp/+datagate/@DataGate/checkLoadStatus.m
dynamo/matlab/mbtools/+mbp/+datagate/@DataGate/configureInspector.m
dynamo/matlab/mbtools/+mbp/+datagate/@DataGate/fetch.m
dynamo/matlab/mbtools/+mbp/+datagate/@DataGate/getBinaryLookout.m
dynamo/matlab/mbtools/+mbp/+datagate/@DataGate/linkStaticProperty.m
dynamo/matlab/mbtools/+mbp/+datagate/@FileGate/FileGate.m
dynamo/matlab/mbtools/+mbp/+datagate/@FileGate/getFilename.m
dynamo/matlab/mbtools/+mbp/+datagate/@FileGate/isAvailable.m
dynamo/matlab/mbtools/+mbp/+datagate/@FileGate/retrieve.m
dynamo/matlab/mbtools/+mbp/+datagate/@FileGate/saveData.m
dynamo/matlab/mbtools/+mbp/+datagate/@FunctionGate/FunctionGate.m
dynamo/matlab/mbtools/+mbp/+datagate/@GateSet/GateSet.m
dynamo/matlab/mbtools/+mbp/+datagate/@GateSet/linesForWorkflowConfigurationFile.m
dynamo/matlab/mbtools/+mbp/+kbfs/+graphs/@GraphManager/GraphManager.m
dynamo/matlab/mbtools/+mbp/+kbfs/@Component/Component.m
dynamo/matlab/mbtools/+mbp/+kbfs/@Component/subsref.m
dynamo/matlab/mbtools/+mbp/+kbfs/@ComponentManager/ComponentManager.m
dynamo/matlab/mbtools/+mbp/+kbfs/@FileStructure/FileStructure.m
dynamo/matlab/mbtools/+mbp/+kbfs/@KeyManager/KeyManager.m
dynamo/matlab/mbtools/+mbp/+kbfs/@WorkflowRepo/WorkflowRepo.m
dynamo/matlab/mbtools/+mbp/+kbfs/@WorkflowRepo/getFolder.m
dynamo/matlab/mbtools/+mbp/+kbfs/@WorkflowRepo/getLocationInDisk.m
dynamo/matlab/mbtools/+mbp/+kbfs/@WorkflowRepo/linkWorkflow.m
dynamo/matlab/mbtools/+mbp/+logs/@TimeStampedItems/TimeStampedItems.m
dynamo/matlab/mbtools/+mbp/+logs/@TimeStampedItems/addItem.m
dynamo/matlab/mbtools/+mbp/+logs/@TimeStampedItems/line2item.m
dynamo/matlab/mbtools/+mbp/+lookout/@BinaryLookout/BinaryLookout.m
dynamo/matlab/mbtools/+mbp/+lookout/@BinaryLookout/addDatagate.m
dynamo/matlab/mbtools/+mbp/+lookout/@BinaryLookout/addSwitcher.m
dynamo/matlab/mbtools/+mbp/+lookout/@BinaryLookout/checkStateValue.m
dynamo/matlab/mbtools/+mbp/+lookout/@BinaryLookout/listenerResponse.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/Lookout.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/addBinaryLookout.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/checkStateValue.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/evaluate.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/findGates.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/listenerResponse.m
dynamo/matlab/mbtools/+mbp/+lookout/@Lookout/stateComparison.m
dynamo/matlab/mbtools/+mbp/+mac/@IdentityObjectContainer/IdentityObjectContainer.m
dynamo/matlab/mbtools/+mbp/+mac/@IdentityObjectContainer/addItem.m
dynamo/matlab/mbtools/+mbp/+mac/@ObjectContainer/ObjectContainer.m
dynamo/matlab/mbtools/+mbp/+mac/@StepContainer/StepContainer.m
dynamo/matlab/mbtools/+mbp/+track/@StackAnnotation/StackAnnotation.m
dynamo/matlab/mbtools/+mbp/+track/@StackAnnotation/stampGeneral.m
dynamo/matlab/mbtools/+mbparse/+cells/indexedCloud2cell.m
dynamo/matlab/mbtools/+mbparse/+cells/insert.m
dynamo/matlab/mbtools/+mbparse/+files/+absolutePath/isAbsolutePath.m
dynamo/matlab/mbtools/+mbparse/+input/allowDobleMinusEverywhere.m
dynamo/matlab/mbtools/+mbparse/+input/removeMinus.m
dynamo/matlab/mbtools/+mbparse/+input/short2real.m
dynamo/matlab/mbtools/+mbparse/+multicore/@ComputingParameters/ComputingParameters.m
dynamo/matlab/mbtools/+mbparse/+multicore/@ComputingParameters/configure.m
dynamo/matlab/mbtools/+mbparse/+multicore/addParser.m
dynamo/matlab/mbtools/+mbparse/+multicore/checkPhysicalCores.m
dynamo/matlab/mbtools/+mbparse/+multicore/checkPool.m
dynamo/matlab/mbtools/+mbparse/+parameters/+aux/@CheckOutput/CheckOutput.m
dynamo/matlab/mbtools/+mbparse/+parameters/+sets/@AfterUpdateManager/AfterUpdateManager.m
dynamo/matlab/mbtools/+mbparse/+parameters/+sets/@AfterUpdateManager/createParameterListeners.m
dynamo/matlab/mbtools/+mbparse/+parameters/+sets/@Container/Container.m
dynamo/matlab/mbtools/+mbparse/+parameters/+sets/@Container/summary.m
dynamo/matlab/mbtools/+mbparse/+parameters/+supersets/@DynamicAreas/DynamicAreas.m
dynamo/matlab/mbtools/+mbparse/+parameters/+supersets/@DynamicAreas/addArea.m
dynamo/matlab/mbtools/+mbparse/+parameters/@Boolean/Boolean.m
dynamo/matlab/mbtools/+mbparse/+parameters/@DynamicStructure/DynamicStructure.m
dynamo/matlab/mbtools/+mbparse/+parameters/@DynamicStructure/dump.m
dynamo/matlab/mbtools/+mbparse/+parameters/@DynamicStructure/dumpParameters.m
dynamo/matlab/mbtools/+mbparse/+parameters/@String/String.m
dynamo/matlab/mbtools/+mbparse/+parameters/@editField/editField.m
dynamo/matlab/mbtools/+mbparse/+parameters/@enum/enum.m
dynamo/matlab/mbtools/+mbparse/+parameters/@genericParameter/embed.m
dynamo/matlab/mbtools/+mbparse/+parameters/@genericParameter/genericParameter.m
dynamo/matlab/mbtools/+mbparse/+parameters/@genericParameter/setValue.m
dynamo/matlab/mbtools/+mbparse/+parameters/@multipleScalar/multipleScalar.m
dynamo/matlab/mbtools/+mbparse/+parameters/@parameterSet/fillFrom.m
dynamo/matlab/mbtools/+mbparse/+parameters/@parameterSet/fillFromStructure.m
dynamo/matlab/mbtools/+mbparse/+parameters/@parameterSet/getParameters.m
dynamo/matlab/mbtools/+mbparse/+parameters/@parameterSet/parameterSet.m
dynamo/matlab/mbtools/+mbparse/+parameters/@singleScalar/check.m
dynamo/matlab/mbtools/+mbparse/+parameters/@singleScalar/singleScalar.m
dynamo/matlab/mbtools/+mbparse/+parameters/@structure/fillFrom.m
dynamo/matlab/mbtools/+mbparse/+parameters/@structure/structure.m
dynamo/matlab/mbtools/+mbparse/+tables/table2String.m
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dynamo/matlab/mbtools/+mbparse/+waitbar/new.m
dynamo/matlab/mbtools/+mbparse/+waitbar/update.m
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dynamo/matlab/src/+dpkgeom/+rotation/shiftsrotFloatMex.mexa64
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dynamo/matlab/src/+dpkio/+tomo/+binary/readSubtomogramMultiClass.m
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dynamo/matlab/src/+dpktilt/+aux/+chains/@TrackFiller/TrackFiller.m
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dynamo/matlab/src/+dpktilt/+aux/+clouds/+manipulations/cloudMagnitude2comparisonAgainstGroup.m
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dynamo/matlab/src/+dpktilt/+aux/+clouds/+manipulations/countMarkersPerTilt.m
dynamo/matlab/src/+dpktilt/+aux/+clouds/+manipulations/countTiltsPerMarker.m
dynamo/matlab/src/+dpktilt/+aux/+clouds/+manipulations/croppableSubcloud.m
dynamo/matlab/src/+dpktilt/+aux/+clouds/+manipulations/merge.m
dynamo/matlab/src/+dpktilt/+aux/+clouds/+manipulations/setdiff.m
dynamo/matlab/src/+dpktilt/+aux/+clouds/+math/+markerDistribution/numberByBinning.m
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dynamo/matlab/src/+dpktilt/+aux/+clouds/+math/setdiff.m
dynamo/matlab/src/+dpktilt/+aux/+clouds/+select/frames.m
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dynamo/matlab/src/+dpktilt/+aux/+clouds/@Parser/Parser.m
dynamo/matlab/src/+dpktilt/+aux/+detect/+centering/@MarkerCoherence/MarkerCoherence.m
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dynamo/matlab/src/+dpktilt/+aux/+detect/@GoldFinder/GoldFinder.m
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dynamo/matlab/src/+dpktilt/+aux/+detect/@GoldFinder/switchAutosave.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+cloudOverlap/@Shifter/Shifter.m
dynamo/matlab/src/+dpktilt/+aux/+index/+cloudOverlap/@Shifter/compute.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulator/RayAccumulator.m
dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulator/computeKnotContributions.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulator/extractBestUnambiguousSubcloud.m
dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulator/extractionAllUnambiguousSubcloudsIteratively.m
dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulator/getIndexBestKnotWithUnambiguousSubcloud.m
dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulator/getUniqueContributionsPerKnot.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+extensor/@RayAccumulatorManager/rotateCloud.m
dynamo/matlab/src/+dpktilt/+aux/+index/+reprojection/+tiltGaps/@Filler/Filler.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+reprojection/+tiltGaps/@Plotter/Plotter.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+reprojection/@ReindexingProcess/ReindexingProcess.m
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dynamo/matlab/src/+dpktilt/+aux/+index/+trackArrays/charTracks2NumericTracks.m
dynamo/matlab/src/+dpktilt/+aux/+index/+trackArrays/getMaxTilt.m
dynamo/matlab/src/+dpktilt/+aux/+index/@Indexer/Indexer.m
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