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Merge pull request #36 from saalfeldlab/hide-duplicate-options
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Hide duplicate options from synopsis/help message but mention in the global options as appropriate
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@hanslovsky
hanslovsky authored Sep 18, 2019
2 parents 318fa36 + 5272da4 commit d672c51
Showing 1 changed file with 76 additions and 28 deletions.
104 changes: 76 additions & 28 deletions src/main/kotlin/org/janelia/saalfeldlab/paintera/conversion/to/paintera/ToPainteraData.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ class ToPainteraData {

@CommandLine.Command(
name = "to-paintera",
sortOptions = false,
aliases = ["tp"],
usageHelpWidth = 120,
header = [
Expand Down Expand Up @@ -114,26 +115,26 @@ paintera-convert to-paintera \
@CommandLine.ArgGroup(exclusive = false, multiplicity = "0..1")
var parameters: GlobalParameters = GlobalParameters()

@CommandLine.ArgGroup(exclusive = false, multiplicity = "1..*")
lateinit var containers: Array<ContainerParameters>

@CommandLine.Option(names = ["--overwrite-existing"], defaultValue = "false")
var overwriteExisting: Boolean = false

@CommandLine.Option(names = ["--help"], help = true, usageHelp = true)
var helpRequested: Boolean = false

@CommandLine.Option(names = ["--output-container"], required = true, paramLabel = "OUTPUT_CONTAINER")
lateinit var _outputContainer: String

val outputContainer: String
get() = File(_outputContainer).absolutePath

@CommandLine.Option(
names = ["--spark-master"],
required = false)
var sparkMaster: String? = null

@CommandLine.ArgGroup(exclusive = false, multiplicity = "1..*")
lateinit var containers: Array<ContainerParameters>

@CommandLine.Option(names = ["--help"], help = true, usageHelp = true)
var helpRequested: Boolean = false

val outputContainer: String
get() = File(_outputContainer).absolutePath

override fun call(): Int {

if (helpRequested)
Expand Down Expand Up @@ -207,6 +208,7 @@ class GlobalParameters : Callable<Unit> {
// TODO use custom class instead of IntArray
@CommandLine.Option(
names = ["--block-size"],
description = ["Use --container-block-size and --dataset-block-size for container and dataset specific block sizes, respectively."],
paramLabel = SpatialIntArray.PARAM_LABEL,
defaultValue = "64,64,64",
converter = [SpatialIntArray.Converter::class])
Expand All @@ -215,35 +217,75 @@ class GlobalParameters : Callable<Unit> {
@CommandLine.Option(
names = ["--scale"],
arity = "1..*",
description = ["Relative downsampling factors for each level in the format x,y,z, where x,y,z are integers. Single integers u are interpreted as u,u,u"],
description = [
"Relative downsampling factors for each level in the format x,y,z, where x,y,z are integers. Single integers u are interpreted as u,u,u.",
"Use --container-scale and --dataset-scale for container and dataset specific scales, respectively."],
converter = [SpatialIntArray.Converter::class],
paramLabel = SpatialIntArray.PARAM_LABEL)
private lateinit var _scales: Array<SpatialIntArray>

@CommandLine.Option(
names = ["--downsample-block-sizes"],
description = ["Use --container-downsample-block-sizes and --dataset-downsample-block-sizes for container and dataset specific block sizes, respectively."],
arity = "1..*",
converter = [SpatialIntArray.Converter::class],
paramLabel = SpatialIntArray.PARAM_LABEL)
private lateinit var _downsamplingBlockSizes: Array<SpatialIntArray>

@CommandLine.Option(names = ["--revert-array-attributes"], defaultValue = "false")
@CommandLine.Option(
names = ["--revert-array-attributes"],
description = [
"Revert array attributes like resolution and offset, i.e. [x, y, z] -> [z, y, x].",
"Use --container-revert-array-attributes and --dataset-revert-array-attributes for container and dataset specific setting, respectively."],
defaultValue = "false")
var revertArrayAttributes: Boolean = false

@CommandLine.Option(names = ["--resolution"], converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
@CommandLine.Option(
names = ["--resolution"],
description = [
"Specify resolution (overrides attributes of input datasets, if any).",
"Use --container-resolution and --dataset-resolution for container and dataset specific resolution, respectively."],
converter = [SpatialDoubleArray.Converter::class],
paramLabel = SpatialDoubleArray.PARAM_LABEL)
var resolution: SpatialDoubleArray? = null

@CommandLine.Option(names = ["--offset"], converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
@CommandLine.Option(
names = ["--offset"],
description = [
"Specify offset (overrides attributes of input datasets, if any).",
"Use --container-offset and --dataset-offset for container and dataset specific resolution, respectively."],
converter = [SpatialDoubleArray.Converter::class],
paramLabel = SpatialDoubleArray.PARAM_LABEL)
var offset: SpatialDoubleArray? = null

@CommandLine.Option(names = ["--max-num-entries", "-m"], arity = "1..*", paramLabel = "N")
@CommandLine.Option(
names = ["--max-num-entries", "-m"],
description = [
"" +
"Limit number of entries for non-scalar label types by N. If N is negative, do not limit number of entries. " +
"If fewer values than the number of down-sampling layers are provided, the missing values are copied from the " +
"last available entry. If none are provided, default to -1 for all levels.",
"Use --container-max-num-entries and --dataset-max-num-entries for container and dataset specific settings, respectively."],
arity = "1..*",
paramLabel = "N")
private var _maxNumEntries: IntArray? = null

@CommandLine.Option(names = ["--label-block-lookup-n5-block-size"], defaultValue = "10000", paramLabel = "N")
@CommandLine.Option(
names = ["--label-block-lookup-n5-block-size"],
description = [
"Set the block size for the N5 container for the label-block-lookup.",
"Use --container-label-block-lookup-n5-block-size and --dataset-label-block-lookup-n5-block-size for container and dataset specific settings, respectively."],
defaultValue = "10000",
paramLabel = "N")
var labelBlockLookupN5BlockSize: Int = 10000
private set

@CommandLine.Option(names = ["--winner-takes-all-downsampling"], defaultValue = "false")
@CommandLine.Option(
names = ["--winner-takes-all-downsampling"],
description = [
"Use scalar label type with winner-takes-all downsampling.",
"Use --container-winner-takes-all-downsampling and --dataset-winner-takes-all-downsampling for container and dataset specific settings, respectively."],
defaultValue = "false")
var winnerTakesAllDownsampling: Boolean = false
private set

Expand Down Expand Up @@ -327,13 +369,15 @@ class ContainerSpecificParameters {

@CommandLine.Option(
names = ["--container-block-size"],
hidden = true,
paramLabel = SpatialIntArray.PARAM_LABEL,
defaultValue = "64,64,64",
converter = [SpatialIntArray.Converter::class])
private var _blockSize: SpatialIntArray? = null

@CommandLine.Option(
names = ["--container-scale"],
hidden = true,
arity = "1..*",
description = ["Relative downsampling factors for each level in the format x,y,z, where x,y,z are integers. Single integers u are interpreted as u,u,u"],
converter = [SpatialIntArray.Converter::class],
Expand All @@ -342,27 +386,28 @@ class ContainerSpecificParameters {

@CommandLine.Option(
names = ["--container-downsample-block-sizes"],
hidden = true,
arity = "1..*",
converter = [SpatialIntArray.Converter::class],
paramLabel = SpatialIntArray.PARAM_LABEL)
private var _downsamplingBlockSizes: Array<SpatialIntArray>? = null

@CommandLine.Option(names = ["--container-revert-array-attributes"])
@CommandLine.Option(names = ["--container-revert-array-attributes"], hidden = true)
private var _revertArrayAttributes: Boolean? = null

@CommandLine.Option(names = ["--container-resolution"], converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
@CommandLine.Option(names = ["--container-resolution"], hidden = true, converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
private var _resolution: SpatialDoubleArray? = null

@CommandLine.Option(names = ["--container-offset"], converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
@CommandLine.Option(names = ["--container-offset"], hidden = true, converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
private var _offset: SpatialDoubleArray? = null

@CommandLine.Option(names = ["--container-max-num-entries"], arity = "1..*", paramLabel = "N")
@CommandLine.Option(names = ["--container-max-num-entries"], hidden = true, arity = "1..*", paramLabel = "N")
private var _maxNumEntries: IntArray? = null

@CommandLine.Option(names = ["--container-label-block-lookup-n5-block-size"], paramLabel = "N")
@CommandLine.Option(names = ["--container-label-block-lookup-n5-block-size"], hidden = true, paramLabel = "N")
private var _labelBlockLookupN5BlockSize: Int? = null

@CommandLine.Option(names = ["--container-winner-takes-all-downsampling"])
@CommandLine.Option(names = ["--container-winner-takes-all-downsampling"], hidden = true)
private var _winnerTakesAllDownsampling: Boolean? = null

val blockSize: SpatialIntArray
Expand Down Expand Up @@ -412,12 +457,14 @@ class DatasetSpecificParameters {

@CommandLine.Option(
names = ["--dataset-block-size"],
hidden = true,
paramLabel = SpatialIntArray.PARAM_LABEL,
converter = [SpatialIntArray.Converter::class])
private var _blockSize: SpatialIntArray? = null

@CommandLine.Option(
names = ["--dataset-scale"],
hidden = true,
arity = "1..*",
description = ["Relative downsampling factors for each level in the format x,y,z, where x,y,z are integers. Single integers u are interpreted as u,u,u"],
converter = [SpatialIntArray.Converter::class],
Expand All @@ -426,31 +473,32 @@ class DatasetSpecificParameters {

@CommandLine.Option(
names = ["--dataset-downsample-block-sizes"],
hidden = true,
arity = "1..*",
description = ["Relative downsampling factors for each level in the format x,y,z, where x,y,z are integers. Single integers u are interpreted as u,u,u"],
converter = [SpatialIntArray.Converter::class],
paramLabel = SpatialIntArray.PARAM_LABEL)
private var _downsamplingBlockSizes: Array<SpatialIntArray>? = null

@CommandLine.Option(names = ["--dataset-revert-array-attributes"])
@CommandLine.Option(names = ["--dataset-revert-array-attributes"], hidden = true)
private var _revertArrayAttributes: Boolean? = null

@CommandLine.Option(names = ["--dataset-resolution"], converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
@CommandLine.Option(names = ["--dataset-resolution"], hidden = true, converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
private var _resolution: SpatialDoubleArray? = null

@CommandLine.Option(names = ["--dataset-offset"], converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
@CommandLine.Option(names = ["--dataset-offset"], hidden = true, converter = [SpatialDoubleArray.Converter::class], paramLabel = SpatialDoubleArray.PARAM_LABEL)
private var _offset: SpatialDoubleArray? = null

@CommandLine.Option(names = ["--type"], completionCandidates = TypeOptions::class, required = false, paramLabel = "TYPE")
private var _type: String? = null

@CommandLine.Option(names = ["--dataset-max-num-entries"], arity = "1..*", paramLabel = "N")
@CommandLine.Option(names = ["--dataset-max-num-entries"], hidden = true, arity = "1..*", paramLabel = "N")
private var _maxNumEntries: IntArray? = null

@CommandLine.Option(names = ["--dataset-label-block-lookup-n5-block-size"], paramLabel = "N")
@CommandLine.Option(names = ["--dataset-label-block-lookup-n5-block-size"], hidden = true, paramLabel = "N")
private var _labelBlockLookupN5BlockSize: Int? = null

@CommandLine.Option(names = ["--dataset-winner-takes-all-downsampling"])
@CommandLine.Option(names = ["--dataset-winner-takes-all-downsampling"], hidden = true)
private var _winnerTakesAllDownsampling: Boolean? = null

val blockSize: SpatialIntArray
Expand Down

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