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First attempt to add spark ZPositionCorrectionClient for use in pipel…
…ine. The pipeline implementation does not (yet) derive aligned stack names, so zcorr can only be run in isolation with the align stack names explicitly specified.
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89
...-ws-java-client/src/main/java/org/janelia/render/client/parameter/ZSpacingParameters.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,89 @@ | ||
| package org.janelia.render.client.parameter; | ||
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| import com.beust.jcommander.Parameter; | ||
| import com.beust.jcommander.ParametersDelegate; | ||
| import com.fasterxml.jackson.annotation.JsonIgnore; | ||
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| import java.io.FileNotFoundException; | ||
| import java.io.Serializable; | ||
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| import org.janelia.render.client.zspacing.HeadlessZPositionCorrection; | ||
| import org.janelia.render.client.zspacing.loader.ResinMaskParameters; | ||
| import org.janelia.thickness.inference.Options; | ||
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| /** | ||
| * Parameters for cross correlation based z-layer thickness correction. | ||
| * | ||
| * @author Eric Trautman | ||
| */ | ||
| public class ZSpacingParameters | ||
| implements Serializable { | ||
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| @Parameter( | ||
| names = "--scale", | ||
| description = "Scale to render each layer", | ||
| required = true) | ||
| public Double scale; | ||
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| @Parameter( | ||
| names = "--rootDirectory", | ||
| description = "Root directory for all output (e.g. /groups/flyem/data/alignment-ett/zcorr)", | ||
| required = true) | ||
| public String rootDirectory; | ||
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| @Parameter( | ||
| names = "--runName", | ||
| description = "Common run name to include in output path when running array jobs. " + | ||
| "Typically includes the timestamp when the array job was created. " + | ||
| "Omit if not running in an array job context.") | ||
| public String runName; | ||
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| @Parameter( | ||
| names = "--nLocalEstimates", | ||
| description = "Number of local estimates") | ||
| public Integer nLocalEstimates = 1; | ||
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| @ParametersDelegate | ||
| public ResinMaskParameters resin = new ResinMaskParameters(); | ||
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| @Parameter( | ||
| names = "--normalizedEdgeLayerCount", | ||
| description = "The number of layers at the beginning and end of the stack to assign correction " + | ||
| "delta values of 1.0. This hack fixes the stretched or squished corrections the " + | ||
| "solver typically produces for layers at the edges of the stack. " + | ||
| "For Z0720_07m stacks, we set this value to 30. " + | ||
| "Omit to leave the solver correction values as is.") | ||
| public Integer normalizedEdgeLayerCount; | ||
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| @Parameter( | ||
| names = "--solveExisting", | ||
| description = "Specify to load existing correlation data and solve.", | ||
| arity = 0) | ||
| public boolean solveExisting; | ||
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| @Parameter( | ||
| names = "--optionsJson", | ||
| description = "JSON file containing thickness correction options (omit to use default values)") | ||
| public String optionsJson; | ||
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| public Options inferenceOptions; | ||
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| public Options getInferenceOptions() | ||
| throws FileNotFoundException { | ||
| Options options = this.inferenceOptions; | ||
| if (options == null) { | ||
| if(optionsJson == null) { | ||
| options = HeadlessZPositionCorrection.generateDefaultFIBSEMOptions(); | ||
| } else { | ||
| options = Options.read(optionsJson); | ||
| } | ||
| } | ||
| return options; | ||
| } | ||
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| @JsonIgnore | ||
| public int getComparisonRange() | ||
| throws FileNotFoundException { | ||
| return getInferenceOptions().comparisonRange; | ||
| } | ||
| } |
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