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Update setters to accept default values #226

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merged 5 commits into from
Nov 29, 2023
Merged

Update setters to accept default values #226

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5a99e2b
Add reset methods for each option
melissalinkert Oct 5, 2023
b532b77
Add test for options resetting
melissalinkert Oct 20, 2023
b060386
Allow resetting to defaults via picocli
melissalinkert Oct 20, 2023
19f40de
Merge branch 'master' of github.com:glencoesoftware/bioformats2raw in…
melissalinkert Nov 15, 2023
ec390b6
Merge branch 'master' of github.com:glencoesoftware/bioformats2raw in…
melissalinkert Nov 29, 2023
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2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ configurations.all {
dependencies {
implementation 'net.java.dev.jna:jna:5.10.0'
implementation 'ome:formats-gpl:7.0.0'
implementation 'info.picocli:picocli:4.6.1'
implementation 'info.picocli:picocli:4.7.5'
implementation 'com.univocity:univocity-parsers:2.8.4'
implementation 'dev.zarr:jzarr:0.4.2'
// implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT'
Expand Down
150 changes: 94 additions & 56 deletions src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,49 +130,41 @@ public class Converter implements Callable<Integer> {

private Map<String, String> outputOptions;
private volatile Integer pyramidResolutions;
private volatile List<Integer> seriesList = new ArrayList<Integer>();
private volatile List<Integer> seriesList;

private volatile int tileWidth = 1024;
private volatile int tileHeight = 1024;
private volatile int chunkDepth = 1;
private volatile String logLevel = "WARN";
private volatile int tileWidth;
private volatile int tileHeight;
private volatile int chunkDepth;
private volatile String logLevel;
private volatile boolean progressBars = false;
private volatile boolean printVersion = false;

// cap the default worker count at 4, to prevent problems with
// large images that are not tiled
private volatile int maxWorkers =
(int) Math.min(4, Runtime.getRuntime().availableProcessors());

private volatile int maxCachedTiles = 64;
private volatile ZarrCompression compressionType = ZarrCompression.blosc;
private volatile Map<String, Object> compressionProperties =
new HashMap<String, Object>();;
private volatile Class<?>[] extraReaders = new Class[] {
PyramidTiffReader.class, MiraxReader.class,
BioTekReader.class, ND2PlateReader.class
};
private volatile int maxWorkers;
private volatile int maxCachedTiles;
private volatile ZarrCompression compressionType;
private volatile Map<String, Object> compressionProperties;
private volatile Class<?>[] extraReaders;
private volatile boolean omeroMetadata = true;
private volatile boolean nested = true;
private volatile String pyramidName = null;
private volatile String scaleFormatString = "%d/%d";
private volatile String scaleFormatString;
private volatile Path additionalScaleFormatStringArgsCsv;

/** Additional scale format string arguments after parsing. */
private volatile List<String[]> additionalScaleFormatStringArgs;

private volatile DimensionOrder dimensionOrder = DimensionOrder.XYZCT;
private volatile DimensionOrder dimensionOrder;
private volatile File memoDirectory;
private volatile boolean keepMemoFiles = false;
private volatile Downsampling downsampling = Downsampling.SIMPLE;
private volatile Downsampling downsampling;
private volatile boolean overwrite = false;
private volatile Short fillValue = null;
private volatile List<String> readerOptions = new ArrayList<String>();
private volatile List<String> readerOptions;
private volatile boolean noHCS = false;
private volatile boolean noOMEMeta = false;
private volatile boolean noRootGroup = false;
private volatile boolean reuseExistingResolutions = false;
private volatile int minSize = MIN_SIZE;
private volatile int minSize;

/** Scaling implementation that will be used during downsampling. */
private volatile IImageScaler scaler = new SimpleImageScaler();
Expand Down Expand Up @@ -219,11 +211,17 @@ public class Converter implements Callable<Integer> {
@Parameters(
index = "0",
arity = "1",
description = "file to convert"
description = "file to convert",
defaultValue = Option.NULL_VALUE
)
public void setInputPath(String input) {
// this could be expanded later to support files not on disk
inputPath = Paths.get(input);
if (input != null) {
// this could be expanded later to support files not on disk
inputPath = Paths.get(input);
}
else {
inputPath = null;
}
}

/**
Expand All @@ -238,7 +236,8 @@ public void setInputPath(String input) {
"Filesystems. For example, if the output path given " +
"is 's3://my-bucket/some-path' *and* you have an "+
"S3FileSystem implementation in your classpath, then " +
"all files will be written to S3."
"all files will be written to S3.",
defaultValue = Option.NULL_VALUE
)
public void setOutputPath(String output) {
outputLocation = output;
Expand All @@ -256,7 +255,8 @@ public void setOutputPath(String output) {
"to be used as an additional argument to Filesystem " +
"implementations if used. For example, " +
"--output-options=s3fs_path_style_access=true|... " +
"might be useful for connecting to minio."
"might be useful for connecting to minio.",
defaultValue = Option.NULL_VALUE
)
public void setOutputOptions(Map<String, String> options) {
outputOptions = options;
Expand All @@ -266,16 +266,19 @@ public void setOutputOptions(Map<String, String> options) {
* Define the number of resolutions in the generated pyramid.
* By default, the resolution count is calculated based upon
* the input image size. The resolution count includes the
* full-resolution image, so must be greater than 0.
* full-resolution image. If the resolution count is null,
* then the number of resolutions will be calculated automatically.
* If not null, it must be greater than 0.
*
* @param resolutions pyramid resolution count
*/
@Option(
names = {"-r", "--resolutions"},
description = "Number of pyramid resolutions to generate"
description = "Number of pyramid resolutions to generate",
defaultValue = Option.NULL_VALUE
)
public void setResolutions(int resolutions) {
if (resolutions > 0) {
public void setResolutions(Integer resolutions) {
if (resolutions == null || resolutions > 0) {
pyramidResolutions = resolutions;
}
else {
Expand All @@ -294,12 +297,16 @@ public void setResolutions(int resolutions) {
names = {"-s", "--series"},
arity = "0..1",
split = ",",
description = "Comma-separated list of series indexes to convert"
description = "Comma-separated list of series indexes to convert",
defaultValue = Option.NULL_VALUE
)
public void setSeriesList(List<Integer> seriesToConvert) {
if (seriesToConvert != null) {
seriesList = seriesToConvert;
}
else {
seriesList = new ArrayList<Integer>();
}
}

/**
Expand Down Expand Up @@ -394,7 +401,8 @@ public void setLogLevel(String level) {
@Option(
names = {"-p", "--progress"},
description = "Print progress bars during conversion",
help = true
help = true,
defaultValue = "false"
)
public void setProgressBars(boolean useProgressBars) {
progressBars = useProgressBars;
Expand All @@ -409,7 +417,8 @@ public void setProgressBars(boolean useProgressBars) {
@Option(
names = "--version",
description = "Print version information and exit",
help = true
help = true,
defaultValue = "false"
)
public void setPrintVersionOnly(boolean versionOnly) {
printVersion = versionOnly;
Expand All @@ -423,10 +432,15 @@ public void setPrintVersionOnly(boolean versionOnly) {
*/
@Option(
names = {"--max-workers", "--max_workers"},
description = "Maximum number of workers (default: ${DEFAULT-VALUE})"
description = "Maximum number of workers (default: ${DEFAULT-VALUE})",
defaultValue = "4"
)
public void setMaxWorkers(int workers) {
if (workers > 0) {
int availableProcessors = Runtime.getRuntime().availableProcessors();
if (workers > availableProcessors) {
maxWorkers = availableProcessors;
}
else if (workers > 0) {
maxWorkers = workers;
}
else {
Expand Down Expand Up @@ -478,12 +492,16 @@ public void setCompression(ZarrCompression compression) {
names = {"--compression-properties"},
description = "Properties for the chosen compression (see " +
"https://jzarr.readthedocs.io/en/latest/tutorial.html#compressors" +
" )"
" )",
defaultValue = Option.NULL_VALUE
)
public void setCompressionProperties(Map<String, Object> properties) {
if (properties != null) {
compressionProperties = properties;
}
else {
compressionProperties = new HashMap<String, Object>();
}
}

/**
Expand All @@ -498,7 +516,12 @@ public void setCompressionProperties(Map<String, Object> properties) {
arity = "0..1",
split = ",",
description = "Separate set of readers to include; " +
"(default: ${DEFAULT-VALUE})"
"(default: ${DEFAULT-VALUE})",
defaultValue =
"com.glencoesoftware.bioformats2raw.PyramidTiffReader," +
"com.glencoesoftware.bioformats2raw.MiraxReader," +
"com.glencoesoftware.bioformats2raw.BioTekReader," +
"com.glencoesoftware.bioformats2raw.ND2PlateReader"
)
public void setExtraReaders(Class<?>[] extraReaderList) {
if (extraReaderList != null) {
Expand All @@ -518,7 +541,8 @@ public void setExtraReaders(Class<?>[] extraReaderList) {
description = "Whether to calculate minimum and maximum pixel " +
"values. Min/max calculation can result in slower " +
"conversions. If true, min/max values are saved as " +
"OMERO rendering metadata (true by default)"
"OMERO rendering metadata (true by default)",
defaultValue = "false"
)
public void setCalculateOMEROMetadata(boolean noMinMax) {
omeroMetadata = !noMinMax;
Expand All @@ -533,7 +557,8 @@ public void setCalculateOMEROMetadata(boolean noMinMax) {
@Option(
names = "--no-nested", negatable=true,
description = "Whether to use '/' as the chunk path separator " +
"(true by default)"
"(true by default)",
defaultValue = "false"
)
public void setUnnested(boolean unnested) {
nested = !unnested;
Expand All @@ -550,7 +575,8 @@ public void setUnnested(boolean unnested) {
@Option(
names = "--pyramid-name",
description = "Name of pyramid (default: ${DEFAULT-VALUE}) " +
"[Can break compatibility with raw2ometiff]"
"[Can break compatibility with raw2ometiff]",
defaultValue = Option.NULL_VALUE
)
public void setPyramidName(String pyramid) {
pyramidName = pyramid;
Expand All @@ -568,7 +594,8 @@ public void setPyramidName(String pyramid) {
"by any additional arguments brought in from " +
"`--additional-scale-format-string-args` " +
"[Can break compatibility with raw2ometiff] " +
"(default: ${DEFAULT-VALUE})"
"(default: ${DEFAULT-VALUE})",
defaultValue = "%d/%d"
)
public void setScaleFormat(String formatString) {
if (formatString != null) {
Expand All @@ -588,7 +615,8 @@ public void setScaleFormat(String formatString) {
"scale format string mapping the at the corresponding CSV " +
"row index. It is expected that the CSV file contain " +
"exactly the same number of rows as the input file has " +
"series"
"series",
defaultValue = Option.NULL_VALUE
)
public void setAdditionalScaleFormatCSV(Path scaleFormatCSV) {
additionalScaleFormatStringArgsCsv = scaleFormatCSV;
Expand All @@ -601,7 +629,8 @@ public void setAdditionalScaleFormatCSV(Path scaleFormatCSV) {
*/
@Option(
names = "--memo-directory",
description = "Directory used to store .bfmemo cache files"
description = "Directory used to store .bfmemo cache files",
defaultValue = Option.NULL_VALUE
)
public void setMemoDirectory(File memoDir) {
memoDirectory = memoDir;
Expand All @@ -615,7 +644,8 @@ public void setMemoDirectory(File memoDir) {
*/
@Option(
names = "--keep-memo-files",
description = "Do not delete .bfmemo files created during conversion"
description = "Do not delete .bfmemo files created during conversion",
defaultValue = "false"
)
public void setKeepMemoFiles(boolean keepMemos) {
keepMemoFiles = keepMemos;
Expand Down Expand Up @@ -645,7 +675,8 @@ public void setDownsampling(Downsampling downsampleType) {
*/
@Option(
names = "--overwrite",
description = "Overwrite the output directory if it exists"
description = "Overwrite the output directory if it exists",
defaultValue = "false"
)
public void setOverwrite(boolean canOverwrite) {
overwrite = canOverwrite;
Expand All @@ -660,7 +691,8 @@ public void setOverwrite(boolean canOverwrite) {
@Option(
names = "--fill-value",
description = "Default value to fill in for missing tiles (0-255)" +
" (currently .mrxs only)"
" (currently .mrxs only)",
defaultValue = Option.NULL_VALUE
)
public void setFillValue(Short tileFill) {
if (tileFill == null || (tileFill >= 0 && tileFill <= 255)) {
Expand All @@ -682,12 +714,16 @@ public void setFillValue(Short tileFill) {
names = "--options",
split = ",",
description =
"Reader-specific options, in format key=value[,key2=value2]"
"Reader-specific options, in format key=value[,key2=value2]",
defaultValue = Option.NULL_VALUE
)
public void setReaderOptions(List<String> readerOpts) {
if (readerOpts != null) {
readerOptions = readerOpts;
}
else {
readerOptions = new ArrayList<String>();
}
}

/**
Expand All @@ -700,7 +736,8 @@ public void setReaderOptions(List<String> readerOpts) {
*/
@Option(
names = "--no-hcs",
description = "Turn off HCS writing"
description = "Turn off HCS writing",
defaultValue = "false"
)
public void setNoHCS(boolean noHCSWriting) {
noHCS = noHCSWriting;
Expand All @@ -716,7 +753,8 @@ public void setNoHCS(boolean noHCSWriting) {
@Option(
names = "--no-ome-meta-export",
description = "Turn off OME metadata exporting " +
"[Will break compatibility with raw2ometiff]"
"[Will break compatibility with raw2ometiff]",
defaultValue = "false"
)
public void setNoOMEMeta(boolean noOMEMetaWriting) {
noOMEMeta = noOMEMetaWriting;
Expand All @@ -731,8 +769,8 @@ public void setNoOMEMeta(boolean noOMEMetaWriting) {
@Option(
names = "--no-root-group",
description = "Turn off creation of root group and corresponding " +
"metadata [Will break compatibility with raw2ometiff]"

"metadata [Will break compatibility with raw2ometiff]",
defaultValue = "false"
)
public void setNoRootGroup(boolean noRootGroupWriting) {
noRootGroup = noRootGroupWriting;
Expand All @@ -749,8 +787,8 @@ public void setNoRootGroup(boolean noRootGroupWriting) {
@Option(
names = "--use-existing-resolutions",
description = "Use existing sub resolutions from original input format" +
"[Will break compatibility with raw2ometiff]"

"[Will break compatibility with raw2ometiff]",
defaultValue = "false"
)
public void setReuseExistingResolutions(boolean reuse) {
reuseExistingResolutions = reuse;
Expand Down Expand Up @@ -806,7 +844,7 @@ public void setDimensionOrder(DimensionOrder order) {
* @return path to input data
*/
public String getInputPath() {
return inputPath.toString();
return inputPath == null ? null : inputPath.toString();
}

/**
Expand Down
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