Mercurial > repos > imgteam > bioformats2raw
changeset 1:b32f5368e279 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 98bcca8b963b30cf12dd7f659a4a52764c33e7cc
line wrap: on
line diff
--- a/bf2raw.xml Wed Nov 15 15:14:17 2023 +0000 +++ b/bf2raw.xml Wed Nov 22 19:10:25 2023 +0000 @@ -2,7 +2,7 @@ <description>with Bioformats</description> <macros> <token name="@TOOL_VERSION@">0.7.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <edam_operations> <edam_operation>operation_3443</edam_operation> @@ -12,19 +12,19 @@ </requirements> <command><![CDATA[ -if [ ! -d $output.extra_files_path ];then - mkdir -p $output.extra_files_path; +if [ ! -d $output.files_path ];then + mkdir -p $output.files_path; fi; #if str($io_options.input.ext)=='html': - #set dirlist=os.listdir($io_options.input.extra_files_path) + #set dirlist=os.listdir($io_options.input.files_path) #assert len($dirlist) > 0 - #set input_path=os.path.join(str($io_options.input.extra_files_path), str($dirlist[0])) + #set input_path=os.path.join(str($io_options.input.files_path), str($dirlist[0])) #else: #set input_path=$io_options.input #end if -bioformats2raw $input_path $output.extra_files_path/$io_options.output_name +bioformats2raw $input_path $output.files_path/$io_options.output_name #if $bf2raw_params.multiscales['options'] == 'auto': --target-min-size $bf2raw_params.multiscales.min_xy_size #elif $bf2raw_params.multiscales['options'] == 'manual': @@ -47,9 +47,9 @@ ]]></command> <inputs> - <section name="io_options" title="Input-output paths"> + <section name="io_options" title="Input-output paths" expanded="true"> <param name="input" type="data" format="atsf,scn,ali,labels,ffr,jpeg,ndpi,tf8,pty,fff,mnc,vms,mng,xml,pcx,img,pct,ims,bip,ome.xml,bin,flex,his,hdr,mov,psd,spi,ipl,dv,aiix,j2kr,pst,mod,ome.tif,tif,obf,dib,dic,im3,tga,pbm,c01,crw,mrcs,l2d,seq,mdb,cfg,htm,mvd2,arf,vsi,companion.ome,htd,aim,fts,ndpis,r3d.log,nef,res,jpx,ics,rec,nd2,cr2,dcm,mea,ome,lei,lms,j2k,oib,mtb,ima,ets,wlz,pict,sm3,sm2,nrrd,xdce,acff,al3d,zvi,1sc,xys,tiff,pgm,pcoraw,ppm,ipm,set,cxd,ipw,apl,fake,tnb,txt,xv,tf2,ps,log,zip,epsi,j2ki,dicom,top,msr,frm,hed,gif,dm2,dm3,dm4,zpo,wav,wat,2fl,sdt,liff,hx,pic,ome.btf,am,bmp,pnl,r3d_d3d,jpf,png,tfr,dti,nii.gz,cif,fdf,grey,df3,stk,fli,hdf,btf,stp,ch5,v,sld,ids,dv.log,jpk,mrw,r3d,xlog,ano,jpe,sxm,jpg,vws,raw,czi,spl,avi,ome.tf8,inf,spc,ome.tf2,spe,lsm,afm,lif,naf,afi,inr,lim,nd,tim,html,sif,env,tif,csv,map,nii,gel,ome.tiff,oif,par,amiramesh,pr3,fits,lut,jp2,oir,dat,aisf,zfr,zfp,xqd,eps,xqf,st,nhdr,i2i,thm,exp,svs,mrc" label="Input image located in Galaxy history"/> - <param name="output_name" type="text" value="data.zarr" label="Output zarr data"/> + <param name="output_name" type="text" value="output.ome.zarr" label="Output zarr data"/> </section> <section name="bf2raw_params" title="Parameters fed to file conversion module"> <conditional name="multiscales" > @@ -106,17 +106,17 @@ </output> </test> <test expect_num_outputs="1"> - <param name="input" value="astronaut.png"/> - <param name="output_name" value="astronaut.ome.zarr" /> + <param name="input" value="coins.png"/> + <param name="output_name" value="coins.ome.zarr" /> <output name="output" ftype="html"> - <extra_files type="file" name="astronaut.ome.zarr/.zgroup" value="astronaut.ome.zarr/.zgroup" /> + <extra_files type="file" name="coins.ome.zarr/.zgroup" value="coins.ome.zarr/.zgroup" /> </output> </test> <test expect_num_outputs="1"> - <param name="input" value="rocket.jpg"/> - <param name="output_name" value="rocket.ome.zarr" /> + <param name="input" value="camera.jpg"/> + <param name="output_name" value="camera.ome.zarr" /> <output name="output" ftype="html"> - <extra_files type="file" name="rocket.ome.zarr/.zattrs" value="rocket.ome.zarr/.zattrs" /> + <extra_files type="file" name="camera.ome.zarr/.zattrs" value="camera.ome.zarr/.zattrs" /> </output> </test> </tests> @@ -130,4 +130,4 @@ <citations> <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation> </citations> -</tool> \ No newline at end of file +</tool>
--- a/test-data/astronaut.ome.zarr/.zattrs Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "bioformats2raw.layout" : 3 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/.zgroup Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/0/.zattrs Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -{ - "multiscales" : [ { - "metadata" : { - "method" : "loci.common.image.SimpleImageScaler", - "version" : "Bio-Formats 6.13.0" - }, - "axes" : [ { - "name" : "t", - "type" : "time" - }, { - "name" : "c", - "type" : "channel" - }, { - "name" : "z", - "type" : "space" - }, { - "name" : "y", - "type" : "space" - }, { - "name" : "x", - "type" : "space" - } ], - "name" : "astronaut.png", - "datasets" : [ { - "path" : "0", - "coordinateTransformations" : [ { - "scale" : [ 1.0, 1.0, 1.0, 1.0, 1.0 ], - "type" : "scale" - } ] - }, { - "path" : "1", - "coordinateTransformations" : [ { - "scale" : [ 1.0, 1.0, 1.0, 2.0, 2.0 ], - "type" : "scale" - } ] - }, { - "path" : "2", - "coordinateTransformations" : [ { - "scale" : [ 1.0, 1.0, 1.0, 4.0, 4.0 ], - "type" : "scale" - } ] - } ], - "version" : "0.4" - } ], - "omero" : { - "channels" : [ { - "color" : "FF0000", - "coefficient" : 1, - "active" : true, - "label" : "Channel 0", - "window" : { - "min" : 0.0, - "max" : 255.0, - "start" : 0.0, - "end" : 255.0 - }, - "family" : "linear", - "inverted" : false - }, { - "color" : "00FF00", - "coefficient" : 1, - "active" : true, - "label" : "Channel 1", - "window" : { - "min" : 0.0, - "max" : 255.0, - "start" : 0.0, - "end" : 255.0 - }, - "family" : "linear", - "inverted" : false - }, { - "color" : "0000FF", - "coefficient" : 1, - "active" : true, - "label" : "Channel 2", - "window" : { - "min" : 0.0, - "max" : 255.0, - "start" : 0.0, - "end" : 255.0 - }, - "family" : "linear", - "inverted" : false - } ], - "rdefs" : { - "defaultT" : 0, - "model" : "color", - "defaultZ" : 0 - } - } -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/0/.zgroup Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/0/0/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -{ - "chunks" : [ 1, 1, 1, 480, 640 ], - "compressor" : { - "clevel" : 5, - "blocksize" : 0, - "shuffle" : 1, - "cname" : "lz4", - "id" : "blosc" - }, - "dtype" : "|u1", - "fill_value" : 0, - "filters" : null, - "order" : "C", - "shape" : [ 1, 3, 1, 480, 640 ], - "dimension_separator" : "/", - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/0/1/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -{ - "chunks" : [ 1, 1, 1, 240, 320 ], - "compressor" : { - "clevel" : 5, - "blocksize" : 0, - "shuffle" : 1, - "cname" : "lz4", - "id" : "blosc" - }, - "dtype" : "|u1", - "fill_value" : 0, - "filters" : null, - "order" : "C", - "shape" : [ 1, 3, 1, 240, 320 ], - "dimension_separator" : "/", - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/0/2/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -{ - "chunks" : [ 1, 1, 1, 120, 160 ], - "compressor" : { - "clevel" : 5, - "blocksize" : 0, - "shuffle" : 1, - "cname" : "lz4", - "id" : "blosc" - }, - "dtype" : "|u1", - "fill_value" : 0, - "filters" : null, - "order" : "C", - "shape" : [ 1, 3, 1, 120, 160 ], - "dimension_separator" : "/", - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/OME/.zattrs Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "series" : [ "0" ] -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/OME/.zgroup Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/astronaut.ome.zarr/OME/METADATA.ome.xml Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="astronaut.png"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="true" SignificantBits="8" SizeC="3" SizeT="1" SizeX="640" SizeY="480" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/.zattrs Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "bioformats2raw.layout" : 3 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/.zgroup Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/0/.zattrs Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,66 @@ +{ + "multiscales" : [ { + "metadata" : { + "method" : "loci.common.image.SimpleImageScaler", + "version" : "Bio-Formats 6.13.0" + }, + "axes" : [ { + "name" : "t", + "type" : "time" + }, { + "name" : "c", + "type" : "channel" + }, { + "name" : "z", + "type" : "space" + }, { + "name" : "y", + "type" : "space" + }, { + "name" : "x", + "type" : "space" + } ], + "name" : "camera.jpg", + "datasets" : [ { + "path" : "0", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 1.0, 1.0 ], + "type" : "scale" + } ] + }, { + "path" : "1", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 2.0, 2.0 ], + "type" : "scale" + } ] + }, { + "path" : "2", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 4.0, 4.0 ], + "type" : "scale" + } ] + } ], + "version" : "0.4" + } ], + "omero" : { + "channels" : [ { + "color" : "808080", + "coefficient" : 1, + "active" : true, + "label" : "Channel 0", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + } ], + "rdefs" : { + "defaultT" : 0, + "model" : "greyscale", + "defaultZ" : 0 + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/0/.zgroup Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/0/0/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 96, 96 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 1, 480, 640 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/0/1/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 96, 96 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 1, 240, 320 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/0/2/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 96, 96 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 1, 120, 160 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/OME/.zattrs Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "series" : [ "0" ] +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/OME/.zgroup Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/camera.ome.zarr/OME/METADATA.ome.xml Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,1 @@ +<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="camera.jpg"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="640" SizeY="480" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/.zattrs Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "bioformats2raw.layout" : 3 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/.zgroup Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/0/.zattrs Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,66 @@ +{ + "multiscales" : [ { + "metadata" : { + "method" : "loci.common.image.SimpleImageScaler", + "version" : "Bio-Formats 6.13.0" + }, + "axes" : [ { + "name" : "t", + "type" : "time" + }, { + "name" : "c", + "type" : "channel" + }, { + "name" : "z", + "type" : "space" + }, { + "name" : "y", + "type" : "space" + }, { + "name" : "x", + "type" : "space" + } ], + "name" : "coins.png", + "datasets" : [ { + "path" : "0", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 1.0, 1.0 ], + "type" : "scale" + } ] + }, { + "path" : "1", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 2.0, 2.0 ], + "type" : "scale" + } ] + }, { + "path" : "2", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 4.0, 4.0 ], + "type" : "scale" + } ] + } ], + "version" : "0.4" + } ], + "omero" : { + "channels" : [ { + "color" : "808080", + "coefficient" : 1, + "active" : true, + "label" : "Channel 0", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + } ], + "rdefs" : { + "defaultT" : 0, + "model" : "greyscale", + "defaultZ" : 0 + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/0/.zgroup Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/0/0/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 96, 96 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 1, 480, 640 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/0/1/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 96, 96 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 1, 240, 320 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/0/2/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 96, 96 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 1, 120, 160 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/OME/.zattrs Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "series" : [ "0" ] +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/OME/.zgroup Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coins.ome.zarr/OME/METADATA.ome.xml Wed Nov 22 19:10:25 2023 +0000 @@ -0,0 +1,1 @@ +<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="coins.png"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="640" SizeY="480" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME> \ No newline at end of file
--- a/test-data/rocket.ome.zarr/.zattrs Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "bioformats2raw.layout" : 3 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/.zgroup Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/0/.zattrs Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -{ - "multiscales" : [ { - "metadata" : { - "method" : "loci.common.image.SimpleImageScaler", - "version" : "Bio-Formats 6.13.0" - }, - "axes" : [ { - "name" : "t", - "type" : "time" - }, { - "name" : "c", - "type" : "channel" - }, { - "name" : "z", - "type" : "space" - }, { - "name" : "y", - "type" : "space" - }, { - "name" : "x", - "type" : "space" - } ], - "name" : "rocket.jpg", - "datasets" : [ { - "path" : "0", - "coordinateTransformations" : [ { - "scale" : [ 1.0, 1.0, 1.0, 1.0, 1.0 ], - "type" : "scale" - } ] - }, { - "path" : "1", - "coordinateTransformations" : [ { - "scale" : [ 1.0, 1.0, 1.0, 2.0, 2.0 ], - "type" : "scale" - } ] - }, { - "path" : "2", - "coordinateTransformations" : [ { - "scale" : [ 1.0, 1.0, 1.0, 4.0, 4.0 ], - "type" : "scale" - } ] - } ], - "version" : "0.4" - } ], - "omero" : { - "channels" : [ { - "color" : "FF0000", - "coefficient" : 1, - "active" : true, - "label" : "Channel 0", - "window" : { - "min" : 0.0, - "max" : 255.0, - "start" : 0.0, - "end" : 255.0 - }, - "family" : "linear", - "inverted" : false - }, { - "color" : "00FF00", - "coefficient" : 1, - "active" : true, - "label" : "Channel 1", - "window" : { - "min" : 0.0, - "max" : 255.0, - "start" : 0.0, - "end" : 255.0 - }, - "family" : "linear", - "inverted" : false - }, { - "color" : "0000FF", - "coefficient" : 1, - "active" : true, - "label" : "Channel 2", - "window" : { - "min" : 0.0, - "max" : 255.0, - "start" : 0.0, - "end" : 255.0 - }, - "family" : "linear", - "inverted" : false - } ], - "rdefs" : { - "defaultT" : 0, - "model" : "color", - "defaultZ" : 0 - } - } -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/0/.zgroup Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/0/0/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -{ - "chunks" : [ 1, 1, 1, 427, 640 ], - "compressor" : { - "clevel" : 5, - "blocksize" : 0, - "shuffle" : 1, - "cname" : "lz4", - "id" : "blosc" - }, - "dtype" : "|u1", - "fill_value" : 0, - "filters" : null, - "order" : "C", - "shape" : [ 1, 3, 1, 427, 640 ], - "dimension_separator" : "/", - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/0/1/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -{ - "chunks" : [ 1, 1, 1, 213, 320 ], - "compressor" : { - "clevel" : 5, - "blocksize" : 0, - "shuffle" : 1, - "cname" : "lz4", - "id" : "blosc" - }, - "dtype" : "|u1", - "fill_value" : 0, - "filters" : null, - "order" : "C", - "shape" : [ 1, 3, 1, 213, 320 ], - "dimension_separator" : "/", - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/0/2/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -{ - "chunks" : [ 1, 1, 1, 106, 160 ], - "compressor" : { - "clevel" : 5, - "blocksize" : 0, - "shuffle" : 1, - "cname" : "lz4", - "id" : "blosc" - }, - "dtype" : "|u1", - "fill_value" : 0, - "filters" : null, - "order" : "C", - "shape" : [ 1, 3, 1, 106, 160 ], - "dimension_separator" : "/", - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/OME/.zattrs Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "series" : [ "0" ] -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/OME/.zgroup Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -{ - "zarr_format" : 2 -} \ No newline at end of file
--- a/test-data/rocket.ome.zarr/OME/METADATA.ome.xml Wed Nov 15 15:14:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="rocket.jpg"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="640" SizeY="427" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME> \ No newline at end of file
--- a/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -1,5 +1,5 @@ { - "chunks" : [ 1, 1, 1, 263, 263 ], + "chunks" : [ 1, 1, 1, 96, 96 ], "compressor" : { "clevel" : 5, "blocksize" : 0,
--- a/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/1/.zarray Wed Nov 15 15:14:17 2023 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/1/.zarray Wed Nov 22 19:10:25 2023 +0000 @@ -1,5 +1,5 @@ { - "chunks" : [ 1, 1, 1, 131, 131 ], + "chunks" : [ 1, 1, 1, 96, 96 ], "compressor" : { "clevel" : 5, "blocksize" : 0,