Buildmanager (nornir_buildmanager)ΒΆ

Note: Certain arguments support regular expressions. See the python re module for instructions on how to construct appropriate regular expressions.

Options available to all build commands. Specific pipelines may extend the argument list.

usage: nornir_build volumepath [-h] [-debug] [-lowpriority] [-verbose]
                               volumepath
                               {ImportIDoc,ImportPMG,ImportSectionsImages,ImportDM4,Prune,SetPruneCutoff,ShadeCorrect,RenameFilter,SetFilterMaskName,Histogram,AdjustContrast,ListFilterContrast,SetContrast,SetFilterLock,Mosaic,MosaicNoTranslate,SetMosaicLock,Assemble,AssembleTiles,MosaicReport,StosReport,ListDamagedSections,MarkSectionsDamaged,MarkSectionsUndamaged,CreateVikingXML,Cleanup,CreateBlobFilter,AlignSections,AssembleStosOverlays,SelectBestRegistrationChain,RefineSectionAlignment,ScaleVolumeTransforms,SliceToVolume,VolumeImage,MosaicToVolume,ExportImages}
                               ...
Positional arguments:
volumepath Directory containing volume to execute command on
Options:
-debug=False If true any exceptions raised by pipelines are not handled.
-lowpriority=False, -lp=False
 Run the build with lower priority. The machine may be more responsive at the expense of much slower builds. 3x-5x slower in tests.
-verbose=False Provide additional output
Sub-commands:
ImportIDoc
usage: nornir_build volumepath ImportIDoc [-h] [-to [TO [TO ...]]]
                                          [-cc [CC [CC ...]]] [-ext EXTENSION]
                                          ImportDir
Positional arguments:
ImportDir Directory to import from
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-ext=idoc Extension of idoc files, default is idoc
ImportPMG
usage: nornir_build volumepath ImportPMG [-h] [-to [TO [TO ...]]]
                                         [-cc [CC [CC ...]]] [-ext EXTENSION]
                                         ImportDir
Positional arguments:
ImportDir Directory to import from
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-ext=pmg Extension of pmg files, default is pmg
ImportSectionsImages
usage: nornir_build volumepath ImportSectionsImages [-h] [-to [TO [TO ...]]]
                                                    [-cc [CC [CC ...]]]
                                                    [-ext EXTENSION]
                                                    ImportDir
Positional arguments:
ImportDir Directory to import from
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-ext=png Extension of image files, default is png
ImportDM4
usage: nornir_build volumepath ImportDM4 [-h] [-to [TO [TO ...]]]
                                         [-cc [CC [CC ...]]] [-ext EXTENSION]
                                         ImportDir
Positional arguments:
ImportDir Directory to import from
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-ext=dm4 Extension of digital micrograph version 4 files, default is dm4
Prune
usage: nornir_build volumepath Prune [-h] [-to [TO [TO ...]]]
                                     [-cc [CC [CC ...]]] [-Sections SECTIONS]
                                     [-Channels CHANNELSREGEX] -Threshold
                                     PRUNETHRESHOLD [-InputFilter INPUTFILTER]
                                     [-Downsample DOWNSAMPLE]
                                     [-InputTransform INPUTTRANSFORM]
                                     [-OutputTransform OUTPUTTRANSFORM]
                                     [-overlap OVERLAP]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-Threshold=0 Texture complexity threshold
-InputFilter=Raw8
 Filter to calculate complexity upon
-Downsample=1 Tiles are downsampled by this factor before being scored
-InputTransform=Stage
 Mosaic transform to prune. The transform provides the list of tiles in the mosaic.
-OutputTransform=Prune
 Name of output transform. Contains tiles from input transform minus tiles below threshold.
-overlap=0.1 Percentage overlap between tiles, 0.0 to 1,0
SetPruneCutoff
usage: nornir_build volumepath SetPruneCutoff [-h] [-to [TO [TO ...]]]
                                              [-cc [CC [CC ...]]] -Value
                                              PRUNEVAL -Sections SECTIONS
                                              [-Channels CHANNELREGEX]
                                              [-Filters FILTERREGEX]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Value=0 Prune threshold to set
-Sections Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to be edited
-Filters=* Regular expression describing filters to be edited
ShadeCorrect
usage: nornir_build volumepath ShadeCorrect [-h] [-to [TO [TO ...]]]
                                            [-cc [CC [CC ...]]]
                                            [-Sections SECTIONS]
                                            [-Channels CHANNELSREGEX]
                                            [-Filters FILTERSREGEX]
                                            [-OutputFilter OUTPUTFILTER]
                                            -Correction
                                            {brightfield,darkfield}
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-Filters=(?![M|m]ask)
 Regular expression describing filters to include, * processes all filters
-OutputFilter=ShadingCorrected
 Prefix added to output filters
-Correction=brightfield
 

Brightfield images have a light background with darker features. Darkfield images have a dark background with light features.

Possible choices: brightfield, darkfield

RenameFilter
usage: nornir_build volumepath RenameFilter [-h] [-to [TO [TO ...]]]
                                            [-cc [CC [CC ...]]] -InputFilter
                                            INPUTFILTER -OutputFilter NEWNAME
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-InputFilter Old Filter name
-OutputFilter New Filter name
SetFilterMaskName
usage: nornir_build volumepath SetFilterMaskName [-h] [-to [TO [TO ...]]]
                                                 [-cc [CC [CC ...]]]
                                                 -InputFilter INPUTFILTER
                                                 -MaskName NEWNAME
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-InputFilter Old Filter name
-MaskName New Mask Name for filter name
Histogram
usage: nornir_build volumepath Histogram [-h] [-to [TO [TO ...]]]
                                         [-cc [CC [CC ...]]]
                                         [-Sections SECTIONS]
                                         [-Channels CHANNELSREGEX]
                                         [-Filters FILTERSREGEX]
                                         -InputTransform INPUTTRANSFORM
                                         [-Downsample DOWNSAMPLE]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-Filters=(?![M|m]ask)
 Regular expression describing filters to include, * processes all filters
-InputTransform=Prune
 The transform provided the list of tiles in the mosaic.
-Downsample=1 Use downsampled tiles for faster histogram calculation
AdjustContrast
usage: nornir_build volumepath AdjustContrast [-h] [-to [TO [TO ...]]]
                                              [-cc [CC [CC ...]]]
                                              [-Sections SECTIONS]
                                              [-Channels CHANNELSREGEX]
                                              [-Gamma GAMMA]
                                              [-MinCutoff MINCUTOFF]
                                              [-MaxCutoff MAXCUTOFF]
                                              -InputFilter INPUTFILTER
                                              [-OutputFilter OUTPUTFILTER]
                                              -InputTransform INPUTTRANSFORM
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-Gamma Gamma value for intensity auto-level
-MinCutoff=0.1 Min pixel intensity cutoff as a percentage, 0 to 100
-MaxCutoff=0.5 Max pixel intensity cutoff as a percentage, 0 to 100. Specifying ‘1’ puts the cutoff at 99% of the maximum pixel intensity value.
-InputFilter=Raw8
 Filter to draw images from
-OutputFilter=Leveled
 Filter to draw images from
-InputTransform=Prune
 Mosaic transform to prune. The transform provides the list of tiles in the mosaic.
ListFilterContrast
usage: nornir_build volumepath ListFilterContrast [-h] [-to [TO [TO ...]]]
                                                  [-cc [CC [CC ...]]]
                                                  [-Sections SECTIONS]
                                                  [-Channels CHANNELSREGEX]
                                                  [-Filters FILTERSREGEX]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-Filters=(?![M|m]ask)
 Regular expression describing filters to include, * processes all filters
SetContrast
usage: nornir_build volumepath SetContrast [-h] [-to [TO [TO ...]]]
                                           [-cc [CC [CC ...]]] [-Min MINVALUE]
                                           [-Max MAXVALUE] [-Gamma GAMMAVALUE]
                                           -Sections SECTIONS
                                           [-Channels CHANNELREGEX]
                                           [-Filters FILTERREGEX]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Min=NaN Min intensity value, set to 0 in output
-Max=NaN Max intensity value, set to 1 in output
-Gamma=NaN Gamma adjustment
-Sections Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to be edited
-Filters=* Regular expression describing filters to be edited
SetFilterLock
usage: nornir_build volumepath SetFilterLock [-h] [-to [TO [TO ...]]]
                                             [-cc [CC [CC ...]]] -Locked
                                             LOCKED -Sections SECTIONS
                                             [-Channels CHANNELREGEX]
                                             [-Filters FILTERREGEX]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Locked Lock value, 0 = unlocked, 1 = locked
-Sections Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to be edited
-Filters=* Regular expression describing filters to be edited
Mosaic
usage: nornir_build volumepath Mosaic [-h] [-to [TO [TO ...]]]
                                      [-cc [CC [CC ...]]] [-Sections SECTIONS]
                                      [-Channels CHANNELSREGEX]
                                      [-RegistrationDownsample DOWNSAMPLE]
                                      [-MaxOffset MAXOFFSET] -InputFilter
                                      INPUTFILTER
                                      [-InputTransform INPUTTRANSFORMNAME]
                                      [-OutputTransform OUTPUTTRANSFORMNAME]
                                      [-Iterations ITERATIONS]
                                      [-Threshold DISPLACEMENTTHRESHOLD]
                                      [-CellArea CELLAREA]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-RegistrationDownsample=4
 Downsample level to use for ir-tools
-MaxOffset=0.5 Comma separated list of downsample levels used for assembling output images
-InputFilter=Raw8
 Filter to use for registration
-InputTransform=Prune
 Name of the input transform
-OutputTransform=Grid
 Name of output transform.
-Iterations=10 Maximum number of refinement passes to run
-Threshold=0.25
 Displacement threshold for control point movement. Refinement stops below this value
-CellArea=128 Size of region around each grid point to register, in pixels
MosaicNoTranslate
usage: nornir_build volumepath MosaicNoTranslate [-h] [-to [TO [TO ...]]]
                                                 [-cc [CC [CC ...]]]
                                                 [-Sections SECTIONS]
                                                 [-Channels CHANNELSREGEX]
                                                 [-RegistrationDownsample DOWNSAMPLE]
                                                 [-MaxOffset MAXOFFSET]
                                                 -InputFilter INPUTFILTER
                                                 [-InputTransform INPUTTRANSFORMNAME]
                                                 [-OutputTransform OUTPUTTRANSFORMNAME]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to include, * processes all channels
-RegistrationDownsample=4
 Downsample level to use for ir-tools
-MaxOffset=0.5 Comma separated list of downsample levels used for assembling output images
-InputFilter=Raw8
 Filter to use for registration
-InputTransform=Prune
 Name of the input transform
-OutputTransform=Grid
 Name of output transform.
SetMosaicLock
usage: nornir_build volumepath SetMosaicLock [-h] [-to [TO [TO ...]]]
                                             [-cc [CC [CC ...]]] -Locked
                                             LOCKED -Sections SECTIONS
                                             [-Channels CHANNELREGEX]
                                             -Transforms TRANSFORMREGEX
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Locked Lock value, 0 = unlocked, 1 = locked
-Sections Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to be edited
-Transforms Regular expression describing transform names to be edited
Assemble
usage: nornir_build volumepath Assemble [-h] [-to [TO [TO ...]]]
                                        [-cc [CC [CC ...]]]
                                        [-Sections SECTIONS]
                                        [-Downsample LEVELS] [-NoInterlace]
                                        [-Channels CHANNELREGEX]
                                        [-ChannelPrefix OUTPUTCHANNELPREFIX]
                                        [-Filters FILTERREGEX]
                                        [-Transform TRANSFORMNAME]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Downsample=1 Comma separated list of downsample levels for assembling images. If output is desired only one downsample level can be used.
-NoInterlace=True
 Setting this flag skips the interlace step after assemble. Interlaced images load faster on web pages, but are larger than non-interlaced images.
-Channels=* Regular expression describing channels to be assembled
-ChannelPrefix=
 Create a new channel for the output with this prefix and the name of the input.
-Filters=(?![M|m]ask)
 Regular expression describing filters to be assembled
-Transform=Grid
 Directory to move assembled images to
AssembleTiles
usage: nornir_build volumepath AssembleTiles [-h] [-to [TO [TO ...]]]
                                             [-cc [CC [CC ...]]]
                                             [-Sections SECTIONS]
                                             [-Channels CHANNELREGEX]
                                             [-Filters FILTERREGEX]
                                             [-Transform TRANSFORMNAME]
                                             [-Downsample DOWNSAMPLE]
                                             [-Shape SHAPE]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to be assembled
-Filters=(?![M|m]ask)
 Regular expression describing filters to be assembled
-Transform=Grid
 Transform defining images into mosaic
-Downsample=1 Comma separated list of downsample levels for assembling output images
-Shape=256,256 The size the tiles passed as a comma-delimited pair of integers. For example 256,512. If a single number is passed it is used for both dimensions
MosaicReport
usage: nornir_build volumepath MosaicReport [-h] [-to [TO [TO ...]]]
                                            [-cc [CC [CC ...]]]
                                            [-PruneFilter PRUNEFILTER]
                                            [-ContrastFilter CONTRASTFILTER]
                                            [-AssembleFilter ASSEMBLEFILTER]
                                            [-AssembleDownsample ASSEMBLEDOWNSAMPLE]
                                            [-Output OUTPUTPATH]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-PruneFilter=Raw8
 Input filter passed to Prune pipeline
-ContrastFilter=Raw8
 Input filter passed to Adjust Contrast pipeline
-AssembleFilter=Raw8
 Input filter passed to Assemble or Mosaic pipeline
-AssembleDownsample=1
 Downsample level to build assembled image thumbnails from
-Output=ImageReport
 Name of report html file
StosReport
usage: nornir_build volumepath StosReport [-h] [-to [TO [TO ...]]]
                                          [-cc [CC [CC ...]]] -StosGroup
                                          STOSGROUP
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-StosGroup Stos group to pull images from
ListDamagedSections
usage: nornir_build volumepath ListDamagedSections [-h] [-to [TO [TO ...]]]
                                                   [-cc [CC [CC ...]]]
                                                   [-Block BLOCKREGEX]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Block=* Regular expression describing blocks to include, * processes all blocks
MarkSectionsDamaged
usage: nornir_build volumepath MarkSectionsDamaged [-h] [-to [TO [TO ...]]]
                                                   [-cc [CC [CC ...]]]
                                                   [-Block BLOCKREGEX]
                                                   [-Sections SECTIONS]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Block=* Regular expression describing blocks to include, * processes all blocks
-Sections Section numbers that should not be used as control sections. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
MarkSectionsUndamaged
usage: nornir_build volumepath MarkSectionsUndamaged [-h] [-to [TO [TO ...]]]
                                                     [-cc [CC [CC ...]]]
                                                     [-Block BLOCKREGEX]
                                                     [-Sections SECTIONS]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Block=* Regular expression describing blocks to include, * processes all blocks
-Sections Section numbers to remove from the damaged list. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
CreateVikingXML
usage: nornir_build volumepath CreateVikingXML [-h] [-to [TO [TO ...]]]
                                               [-cc [CC [CC ...]]]
                                               [-StosGroup STOSGROUP]
                                               [-StosMap STOSMAP] [-Host HOST]
                                               -OutputFile OUTPUTFILE
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-StosGroup Stos group to pull images from. If not specified only unregistered mosaics are included.
-StosMap Slice-to-slice mapping of transforms. If not specified only unregistered mosaics are included.
-Host Url of volume, overrides the about.xml settings
-OutputFile Name of file to write .VikingXML is appended to name automatically
Cleanup
usage: nornir_build volumepath Cleanup [-h] [-to [TO [TO ...]]]
                                       [-cc [CC [CC ...]]]
                                       [-Sections SECTIONS]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
CreateBlobFilter
usage: nornir_build volumepath CreateBlobFilter [-h] [-to [TO [TO ...]]]
                                                [-cc [CC [CC ...]]]
                                                [-Sections SECTIONS]
                                                [-Channels CHANNELREGEX]
                                                -InputFilter INPUTFILTER
                                                [-Levels BLOBDOWNSAMPLELEVELS]
                                                [-Radius BLOBRADIUS]
                                                [-Median BLOBMEDIAN]
                                                [-Max BLOBMAX]
                                                [-OutputFilter OUTPUTFILTERNAME]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Sections Section to execute blob on. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
-Channels=* Regular expression describing channels to be assembled
-InputFilter=Leveled
 Name of filter to create blob filter for
-Levels=1 Downsample levels to be blobbed
-Radius=9 Radius to calculate variance within
-Median=7 Median filter radius for input
-Max=3 Max variance before cropping
-OutputFilter=Blob
 Prefix added to created filters
AlignSections
usage: nornir_build volumepath AlignSections [-h] [-to [TO [TO ...]]]
                                             [-cc [CC [CC ...]]]
                                             [-Center CENTER]
                                             [-NumAdjacentSections NUMADJACENTSECTIONS]
                                             [-Channels CHANNELSREGEX]
                                             [-Filters FILTERSREGEX]
                                             [-UseMasks] -Downsample
                                             STOSBRUTEDOWNSAMPLE
                                             [-OutputStosMap OUTPUTSTOSMAP]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Center Center section of the volume. Defaults to center if unspecified. The first run center is saved in meta-data and re-used on later runs.
-NumAdjacentSections=1
 Number of adjacent sections to attempt registration with.
-Channels=* Regular expression describing channels to be aligned
-Filters=(?![M|m]ask)
 Regular expression describing filters to be aligned
-UseMasks=False
 Use masks for images if they are available. Masked areas are replaced with random noise for alignment purposes.
-Downsample=1 Amount to downsample input images before attempting alignment. Images are padded to the next power of two for the FFT. Large images, roughly greater than 2048x2048, can be very slow.
-OutputStosMap=PotentialRegistrationChain
 Name assigned to generated stos map.
AssembleStosOverlays
usage: nornir_build volumepath AssembleStosOverlays [-h] [-to [TO [TO ...]]]
                                                    [-cc [CC [CC ...]]]
                                                    -StosGroup STOSGROUP
                                                    -Downsample
                                                    INPUTDOWNSAMPLE -StosMap
                                                    STOSMAP
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-StosGroup=StosBrute
 Stos group to assemble
-Downsample Downsample level to assemble
-StosMap=FinalStosMap
 Name assigned to generated stos map.
SelectBestRegistrationChain
usage: nornir_build volumepath SelectBestRegistrationChain [-h]
                                                           [-to [TO [TO ...]]]
                                                           [-cc [CC [CC ...]]]
                                                           -StosGroup
                                                           STOSGROUP
                                                           -Downsample
                                                           INPUTDOWNSAMPLE
                                                           -InputStosMap
                                                           INPUTSTOSMAP
                                                           [-OutputStosMap OUTPUTSTOSMAP]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-StosGroup=StosBrute
 Stos group to assemble
-Downsample Downsample level to assemble
-InputStosMap=PotentialRegistrationChain
 Name assigned to generated stos map.
-OutputStosMap=FinalStosMap
 Name assigned to generated stos map.
RefineSectionAlignment
usage: nornir_build volumepath RefineSectionAlignment [-h] [-to [TO [TO ...]]]
                                                      [-cc [CC [CC ...]]]
                                                      [-SectionMap STOSMAP]
                                                      [-InputGroup INPUTGROUP]
                                                      -InputDownsample
                                                      INPUTDOWNSAMPLE
                                                      [-OutputGroup OUTPUTGROUP]
                                                      -OutputDownsample
                                                      OUTPUTDOWNSAMPLE
                                                      [-Filters FILTERSREGEX]
                                                      [-UseMasks]
                                                      [-Threshold DISPLACEMENTTHRESHOLD]
                                                      [-Spacing GRIDSPACING]
                                                      [-CellArea CELLAREA]
                                                      [-Iterations ITERATIONS]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-SectionMap=FinalStosMap
 Map describing which sections register to each other
-InputGroup=StosBrute
 Map describing which sections register to each other
-InputDownsample
 Downsample level to use for input
-OutputGroup=StosGrid
 Name of output group
-OutputDownsample
 Downsample level to use for refinement
-Filters=(?![M|m]ask)
 Regular expression describing filters to be aligned
-UseMasks=False
 Use masks for images if they are available. Masked areas are replaced with random noise for alignment purposes.
-Threshold=0.1 Displacement threshold for control point movement. Refinement stops below this value
-Spacing=128 Grid spacing in pixels
-CellArea=128 Size of region around each grid point to register, in pixels
-Iterations=10 Maximum number of refinement passes to run
ScaleVolumeTransforms
usage: nornir_build volumepath ScaleVolumeTransforms [-h] [-to [TO [TO ...]]]
                                                     [-cc [CC [CC ...]]]
                                                     [-InputGroup SCALEGROUPNAME]
                                                     -InputDownsample
                                                     SCALEINPUTDOWNSAMPLE
                                                     [-OutputDownsample SCALEOUTPUTDOWNSAMPLE]
                                                     [-UseMasks]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-InputGroup=SliceToVolume
 Name of stos group to scale
-InputDownsample
 Downsample level of input stosgroup
-OutputDownsample=1
 Downsample level of output
-UseMasks=False
 Use masks for images if they are available. Masked areas are replaced with random noise for alignment purposes.
SliceToVolume
usage: nornir_build volumepath SliceToVolume [-h] [-to [TO [TO ...]]]
                                             [-cc [CC [CC ...]]]
                                             [-InputDownsample STOVDOWNSAMPLE]
                                             -InputGroup STOVINPUTGROUP
                                             [-OutputGroup STOVOUTPUTGROUPNAME]
                                             [-InputMap INPUTMAP]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-InputDownsample=16
 Downsample level to use for SliceToVolume
-InputGroup=StosGrid
 Map describing which sections register to each other
-OutputGroup=SliceToVolume
 Name of output group
-InputMap=FinalStosMap
 Name of output group
VolumeImage
usage: nornir_build volumepath VolumeImage [-h] [-to [TO [TO ...]]]
                                           [-cc [CC [CC ...]]]
                                           [-InputGroup VOLUMEIMAGEGROUPNAME]
                                           [-InputDownsample VOLUMEIMAGEDOWNSAMPLE]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-InputGroup=SliceToVolume
 Name of stos group to create scaled version of, default = SliceToVolume
-InputDownsample=1
 Downsample level of input stosgroup, default = 1
MosaicToVolume
usage: nornir_build volumepath MosaicToVolume [-h] [-to [TO [TO ...]]]
                                              [-cc [CC [CC ...]]]
                                              [-Channels CHANNELSREGEX]
                                              [-InputDownsample STOSDOWNSAMPLE]
                                              [-InputMap INPUTMAPNAME]
                                              [-InputGroup INPUTSTOSGROUP]
                                              [-InputTransform INPUTTRANSFORMNAME]
                                              [-OutputTransform OUTPUTTRANSFORM]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Channels=* Regular expression describing channels to be processed
-InputDownsample=1
 Downsample level of input stosgroup
-InputMap=SliceToVolume
 Name of output group
-InputGroup=SliceToVolume
 Name of stos group to pass mosaic transforms through
-InputTransform=Grid
 Mosaic transform to pass through slice-to-slice transform
-OutputTransform=ChannelToVolume
 Name of output transform mapping a channel to a volume
ExportImages
usage: nornir_build volumepath ExportImages [-h] [-to [TO [TO ...]]]
                                            [-cc [CC [CC ...]]]
                                            [-Channels CHANNELREGEX]
                                            [-Filters FILTERREGEX]
                                            [-Downsample DOWNSAMPLE]
                                            [-Output OUTPUTPATH]
Options:
-to= E-Mail addresses for reports
-cc= E-Mail addresses for reports
-Channels=* Regular expression describing channels to be assembled
-Filters=(?![M|m]ask)
 Regular expression describing filters to be assembled
-Downsample=1 Downsample output images by this factor
-Output Directory to move assembled images to