MultiFileVolumeListSMImageOutput

MLModule

genre	MultiFileVolumeList, DICOM
author	Wolf Spindler
package	FMEstable/ReleaseMeVis
dll	MLMultiFileVolumeListOutputs
definition	MLMultiFileVolumeListOutputs.def
see also	DirectDicomImport, MultiFileVolumeListBaseOutput, MultiFileVolumeListImageOutput, MultiFileVolumeListRTOutput, MultiFileVolumeListSROutput, FileListFilterPlugin, ImageLoad, MLImageFormatLoad, ImageSave
inherits from	MultiFileVolumeListImageOutput
keywords	DICOM, DCM, import, load, read, slices, overlay, multifile, volume

Purpose

The MultiFileVolumeListSMImageOutput is a dedicated image output for a MultiFileVolumeList, similar to MultiFileVolumeListImageOutput. Additionally MultiFileVolumeListSMImageOutput contains the special output connector output2 for a Whole Slide Image which can be composed from single tiles stored in DICOM images of type Whole Slide Microscopy Data (SM). Also further fields show image property information of that output.

Windows

Default Panel

Input Fields

inputAccessConnector

name: inputAccessConnector, type: MultiFileVolumeListRefCounted(MLBase)

The connector to connect MultiFileVolumeListSMImageOutput with a DirectDicomImport module. If not connected the volume list can be read from a cache file alternatively. This can be switched on or off with Use Base Input.

For accessing this object via scripting, see the Scripting Reference: MLMultiFileVolumeListWrapper.

see also MultiFileVolumeListImageOutput.inputAccessConnector

inputMessageFilterPlugin

name: inputMessageFilterPlugin, type: DicomConfigurableMessageFilter(MLBase)

In some situations is may be of interest to suppress messages (errors, or warnings) generated while loading or importing files since the user is aware of their origin and meaning, and because they shadow other messages which might have a higher importance. For this purpose a plugin can be connected to this input which filters out specific messages, for example a DicomConfigurableMessageFilter. If this input is left open then the messages are generated normally.

see also MultiFileVolumeListImageOutput.inputMessageFilterPlugin

Output Fields

output0

name: output0, type: Image

If the currently selected volume is of an image type then the ML image representation of that volume is provided at this connector. It will be invalid if the imported volume is not of an image type or if it is invalid for other reasons.

see also MultiFileVolumeListImageOutput.output0

output1

name: output1, type: Image

If the currently selected volume is of an image type and if it contains DICOM overlay information then this will be provided at this output. Typically it can be displayed with a SoView2DOverlay on top of the viewer showing the image from output connector 0. If multiple overlays are available, then they will be composed with an OR operation, overlay pixels will have value 1, background pixels 0. This connector will be invalid if no valid DICOM image volume is selected or it does not contain valid overlay information. Only overlays according to the current DICOM standard is displayed; overlays according to the retired DICOM standard are not displayed. See http://medical.nema.org/Dicom/2011/11_03pu.pdf, section C.9 for details. The overlay image data is calculated on demand from the input DICOM information.

see also MultiFileVolumeListImageOutput.output1

outputAccessConnector

name: outputAccessConnector, type: MultiFileVolumeListRefCounted(MLBase)

For accessing this object via scripting, see the Scripting Reference: MLMultiFileVolumeListWrapper.

see MultiFileVolumeListBaseOutput.outputAccessConnector

output2

name: output2, type: Image

Provides the full Whole Slide Image composed from all tiles stored in the MultiFileVolume.

Parameter Fields

Field Index

Annotate: Bool	Ext Y (extY): Integer	Num Vol Voxels (numVolVoxels): Integer
Auto Load Result Cache: Bool	Ext Y (extYFull): Integer	Num Vol Voxels (numVolVoxelsFull): Integer
Cache File Path: String	Ext Z (extZ): Integer	Number of volumes: Integer
Data Type (dataType): String	Ext Z (extZFull): Integer	Related Sequences Source Config: String
Data Type (dataTypeFull): String	Filter: String	Related Volume Indexes: String
Dump Private Tag Values: Bool	First Related Volume Index: Integer	Shared Frame Of Reference Volume Indexes: String
Enable Related Volumes: Bool	First Shared Frame Of Reference Volume Index: Integer	Tag Dump: String
Ext C (extC): Integer	First Volume Index Derived From: Integer	Tag Dump Size: Integer
Ext C (extCFull): Integer	issues: String	updateBaseOutputInformationDone: Trigger
Ext T (extT): Integer	Load Result Cache: Trigger	updateImageOutputInformationDone: Trigger
Ext T (extTFull): Integer	Max Vox Val (maxVoxVal): Double	updateSMImageOutputInformationDone: Trigger
Ext U (extU): Integer	Max Vox Val (maxVoxValFull): Double	Use Base Input: Bool
Ext U (extUFull): Integer	Min Vox Val (minVoxVal): Double	Volume Index: Integer
Ext X (extX): Integer	Min Vox Val (minVoxValFull): Double	Volume Indexes Derived From: String
Ext X (extXFull): Integer	Num shown binary bytes: Integer	Volume Info Dump: String

Visible Fields

Use Base Input

name: useBaseInput, type: Bool, default: TRUE

If enabled then the volume is read from the MultiFileVolumeList (typically provided by a DirectDicomImport) connected to the base input; otherwise the specified cache file is read.

see also MultiFileVolumeListImageOutput.useBaseInput

Load Result Cache

name: loadResultCache, type: Trigger

Loads a volume list from cached result volume.

see also MultiFileVolumeListImageOutput.loadResultCache

Auto Load Result Cache

name: autoLoadResultCache, type: Bool, default: FALSE

If enabled then the cache file is loaded automatically from file.

see also MultiFileVolumeListImageOutput.autoLoadResultCache

Cache File Path

name: cacheFilePath, type: String

File containing a list of cached image volumes.

see also MultiFileVolumeListImageOutput.cacheFilePath

Volume Index

name: outVolIdx, type: Integer, default: 0, minimum: 0

Sets the index of the volume currently selected in the volume list, -1 invalidates output0 and output1.

see also MultiFileVolumeListImageOutput.outVolIdx

Number of volumes

name: numVolumes, type: Integer, default: 0

This read-only field shows number of available volumes.

see also MultiFileVolumeListImageOutput.numVolumes

Volume Info Dump

name: volumeInfoDump, type: String, persistent: no

Shows a collection of available information about the currently selected volume.

see also MultiFileVolumeListImageOutput.volumeInfoDump

Tag Dump Size

name: tagDumpSize, type: Integer, default: 10000

Maximum number of characters shown in the ‘Tag Dump’ field. Too large values can degrade performance when viewing the DICOM tag list.

see also MultiFileVolumeListImageOutput.tagDumpSize

Dump Private Tag Values

name: dumpPrivateTagValues, type: Bool, default: FALSE

If enabled then values of private tags are decoded if decoders are available.

see also MultiFileVolumeListImageOutput.dumpPrivateTagValues

Num shown binary bytes

name: numShownBinaryEntries, type: Integer, default: 8

Number of shown entries of binary tags.

see also MultiFileVolumeListImageOutput.numShownBinaryEntries

Annotate

name: annotate, type: Bool, default: FALSE

If enabled then tags are annotated with further descriptive information such as possible types (1=Mandatory, 1C=Conditionally Mandatory, 2=Mandatory, may have zero or one item, 2C=Conditionally Mandatory, but may be empty, 3=Optional) and possible meanings of the tag. Note that no context analysis is performed for that information and therefore all possible and perhaps redundant meanings are shown.

see also MultiFileVolumeListImageOutput.annotate

Filter

name: regExLineFilter, type: String

see MultiFileVolumeListBaseOutput.regExLineFilter

Tag Dump

name: tagDump, type: String, persistent: no

Shows the DICOM tag list of currently selected volume (the dump will be clamped if the tag list is too large).

see also MultiFileVolumeListImageOutput.tagDump

Ext X (extX)

name: extX, type: Integer, default: 0

This read-only field shows the x-extent of the currently selected volume.

see also MultiFileVolumeListImageOutput.extX

Ext Y (extY)

name: extY, type: Integer, default: 0

This read-only field shows the y-extent of the currently selected volume.

see also MultiFileVolumeListImageOutput.extY

Ext Z (extZ)

name: extZ, type: Integer, default: 0

This read-only field shows the z-extent of the currently selected volume.

see also MultiFileVolumeListImageOutput.extZ

Ext C (extC)

name: extC, type: Integer, default: 0

This read-only field shows the color dimension extent of the currently selected volume.

see also MultiFileVolumeListImageOutput.extC

Ext T (extT)

name: extT, type: Integer, default: 0

This read-only field shows the time dimension extent of the currently selected volume.

see also MultiFileVolumeListImageOutput.extT

Ext U (extU)

name: extU, type: Integer, default: 0

This read-only field shows the u-dimension extent of the currently selected volume.

see also MultiFileVolumeListImageOutput.extU

Num Vol Voxels (numVolVoxels)

name: numVolVoxels, type: Integer, default: 0

This read-only field shows the number of voxels of the currently selected volume.

see also MultiFileVolumeListImageOutput.numVolVoxels

Data Type (dataType)

name: dataType, type: String

This read-only field contains the voxel data type of the currently selected volume.

see also MultiFileVolumeListImageOutput.dataType

Min Vox Val (minVoxVal)

name: minVoxVal, type: Double, default: 0

This read-only field shows the minimum voxel value in the currently selected volume.

see also MultiFileVolumeListImageOutput.minVoxVal

Max Vox Val (maxVoxVal)

name: maxVoxVal, type: Double, default: 0

This read-only field shows the maximum voxel value in the currently selected volume.

see also MultiFileVolumeListImageOutput.maxVoxVal

Enable Related Volumes

name: enableRelatedVolumes, type: Bool, default: FALSE

Disable/enable the calculation of related volume indexes (which may be time consuming on large volume sets).

see also MultiFileVolumeListImageOutput.enableRelatedVolumes

Related Sequences Source Config

name: relatedSequencesSourceConfig, type: String, default: ReferencedSeriesSequence, SourceImageSequence, DerivationImageSequence

A string containing the configuration which determines the sequences in which the ReferencedSOPInstanceUIDs shall be searched which shall be used to search volumes considered as ‘related’. Entries may be separated with spaces or commas inside lines. If multiple entries are inside one line then only the first found one is taken as source. Entries found in newline-separated lines are all scanned for ReferencedSOPInstanceUIDs. Allowed strings are currently

• ReferencedSeriesSequence : Look in ReferencedSeriesSequence -> ReferencedInstanceSequence -> ReferencedImageSequence

• ReferencedImageSequence : Look in ReferencedImageSequence

• SourceImageSequence : Look in SourceImageSequence

• DerivationImageSequence : Look in DerivationImageSequence -> SourceImageSequence

Example: Take ReferencedSOPInstanceUIDs from SourceImageSequence and, only if that one is not found, from ReferencedImageSequence. Then add those from DerivationImageSequence:

SourceImageSequence, ReferencedImageSequence

DerivationImageSequence

see also MultiFileVolumeListImageOutput.relatedSequencesSourceConfig

First Volume Index Derived From

name: firstVolumeIndexDerivedFrom, type: Integer, persistent: no

The module tries to determine the volume(s) (or to be more precise: the frames) from which the image has been derived. If this or these volumes are also part of the volume list connected to the input of this module, then First Volume Index Derived From shows the volume index of the first of these volumes. Note that no, one or multiple of such volumes can exist. The default is -1 if no volume has been found. See also Volume Indexes Derived From.

see also MultiFileVolumeListImageOutput.firstVolumeIndexDerivedFrom

Volume Indexes Derived From

name: volumeIndexesDerivedFrom, type: String, persistent: no

As described for First Volume Index Derived From the module tries to determine the volume(s) (or to be more precise: the frames) from which the image has been derived. If this or these volumes are also part of the volume list connected to the input of this module, then Volume Indexes Derived From shows a space separated list of all these volumes. The default is empty if no volume has been found. See also First Volume Index Derived From.

see also MultiFileVolumeListImageOutput.volumeIndexesDerivedFrom

First Shared Frame Of Reference Volume Index

name: firstSharedFrameOfReferenceVolumeIndex, type: Integer, persistent: no

The module tries to determine the volume(s) (or to be more precise: the frames) which share the same FrameOfReferenceUID. If this or these volumes are also part of the volume list connected to the input of this module, then First Shared Frame Of Reference Volume Index shows the volume index of the first of these volumes. Note that no, one or multiple of such volumes can exist. The default is -1 if no volume has been found. See also Shared Frame Of Reference Volume Indexes.

see also MultiFileVolumeListImageOutput.firstSharedFrameOfReferenceVolumeIndex

Shared Frame Of Reference Volume Indexes

name: sharedFrameOfReferenceVolumeIndexes, type: String, persistent: no

As described for First Shared Frame Of Reference Volume Index the module tries to determine the volume(s) (or to be more precise: the frames) which share the same FrameOfReferenceUID. If this or these volumes are also part of the volume list connected to the input of this module, then Shared Frame Of Reference Volume Indexes shows a space separated list of all these volumes. The default is empty if no volume has been found. See also First Shared Frame Of Reference Volume Index.

see also MultiFileVolumeListImageOutput.sharedFrameOfReferenceVolumeIndexes

First Related Volume Index

name: firstRelatedVolumeIndex, type: Integer, persistent: no

The first valid index from First Volume Index Derived From and First Shared Frame Of Reference Volume Index.

see also MultiFileVolumeListImageOutput.firstRelatedVolumeIndex

Related Volume Indexes

name: relatedVolumeIndexes, type: String, persistent: no

All valid indexes from Volume Indexes Derived From and Shared Frame Of Reference Volume Indexes.

see also MultiFileVolumeListImageOutput.relatedVolumeIndexes

Ext X (extXFull)

name: extXFull, type: Integer, default: 0

This read-only field shows the x-extent of the composed image slide of the currently selected volume.

Ext Y (extYFull)

name: extYFull, type: Integer, default: 0

This read-only field shows the y-extent of the composed image slide of the currently selected volume.

Ext Z (extZFull)

name: extZFull, type: Integer, default: 0

This read-only field shows the z-extent of the composed image slide of the currently selected volume.

Ext C (extCFull)

name: extCFull, type: Integer, default: 0

This read-only field shows the c-extent of the composed image slide of the currently selected volume.

Ext T (extTFull)

name: extTFull, type: Integer, default: 0

This read-only field shows the t-extent of the composed image slide of the currently selected volume.

Ext U (extUFull)

name: extUFull, type: Integer, default: 0

This read-only field shows the y-extent of the composed image slide of the currently selected volume.

Num Vol Voxels (numVolVoxelsFull)

name: numVolVoxelsFull, type: Integer, default: 0

This read-only field shows the number of voxels of the composed image slide of the currently selected volume.

Data Type (dataTypeFull)

name: dataTypeFull, type: String

This read-only field contains the voxel data type of the composed image slide of the currently selected volume.

Min Vox Val (minVoxValFull)

name: minVoxValFull, type: Double, default: 0

This read-only field shows the minimum voxel value in the composed image slide of the currently selected volume.

Max Vox Val (maxVoxValFull)

name: maxVoxValFull, type: Double, default: 0

This read-only field shows the maximum voxel value in the composed image slide of the currently selected volume.

Hidden Fields

issues

name: issues, type: String, persistent: no

see MultiFileVolumeListBaseOutput.issues

updateBaseOutputInformationDone

name: updateBaseOutputInformationDone, type: Trigger

Field which is touched after the completion of updates of all fields belonging to the same class type this field belongs to. Note that derived classes may update their fields later.

see also MultiFileVolumeListImageOutput.updateBaseOutputInformationDone

updateImageOutputInformationDone

name: updateImageOutputInformationDone, type: Trigger

Field which is touched after the completion of updates of all fields belonging to the same class type this field belongs to. Note that derived classes may update their fields later.

see also MultiFileVolumeListImageOutput.updateImageOutputInformationDone

updateSMImageOutputInformationDone

name: updateSMImageOutputInformationDone, type: Trigger

Field which is touched after the completion of updates of all fields belonging to the same class type this field belongs to. Note that derived classes may update their fields later.