# HG changeset patch
# User imgteam
# Date 1700680225 0
# Node ID b32f5368e2792e0e388bac39643a1b95c7282125
# Parent  4b6c2135e54740f789ec583713b44f22acda6095
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 98bcca8b963b30cf12dd7f659a4a52764c33e7cc

diff -r 4b6c2135e547 -r b32f5368e279 bf2raw.xml
--- 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>
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/.zattrs
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/.zgroup
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/.zattrs
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/.zgroup
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/0/.zarray
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/0/0/0/0/0/0
Binary file test-data/astronaut.ome.zarr/0/0/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/0/0/1/0/0/0
Binary file test-data/astronaut.ome.zarr/0/0/0/1/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/0/0/2/0/0/0
Binary file test-data/astronaut.ome.zarr/0/0/0/2/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/1/.zarray
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/1/0/0/0/0/0
Binary file test-data/astronaut.ome.zarr/0/1/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/1/0/1/0/0/0
Binary file test-data/astronaut.ome.zarr/0/1/0/1/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/1/0/2/0/0/0
Binary file test-data/astronaut.ome.zarr/0/1/0/2/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/2/.zarray
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/2/0/0/0/0/0
Binary file test-data/astronaut.ome.zarr/0/2/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/2/0/1/0/0/0
Binary file test-data/astronaut.ome.zarr/0/2/0/1/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/0/2/0/2/0/0/0
Binary file test-data/astronaut.ome.zarr/0/2/0/2/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/OME/.zattrs
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/OME/.zgroup
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.ome.zarr/OME/METADATA.ome.xml
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/astronaut.png
Binary file test-data/astronaut.png has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.jpg
Binary file test-data/camera.jpg has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/.zattrs
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/.zgroup
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/.zattrs
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/.zgroup
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/0/.zarray
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/0/0/0/0/0/0
Binary file test-data/camera.ome.zarr/0/0/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/0/0/0/0/0/1
Binary file test-data/camera.ome.zarr/0/0/0/0/0/0/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/0/0/0/0/0/2
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diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/0/0/0/0/1/0
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diff -r 4b6c2135e547 -r b32f5368e279 test-data/camera.ome.zarr/0/0/0/0/0/1/1
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Binary file test-data/coins.ome.zarr/0/0/0/0/0/4/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/0/0/0/0/4/2
Binary file test-data/coins.ome.zarr/0/0/0/0/0/4/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/0/0/0/0/4/3
Binary file test-data/coins.ome.zarr/0/0/0/0/0/4/3 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/0/0/0/0/4/4
Binary file test-data/coins.ome.zarr/0/0/0/0/0/4/4 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/0/0/0/0/4/5
Binary file test-data/coins.ome.zarr/0/0/0/0/0/4/5 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/0/0/0/0/4/6
Binary file test-data/coins.ome.zarr/0/0/0/0/0/4/6 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/.zarray
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/0/0
Binary file test-data/coins.ome.zarr/0/1/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/0/1
Binary file test-data/coins.ome.zarr/0/1/0/0/0/0/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/0/2
Binary file test-data/coins.ome.zarr/0/1/0/0/0/0/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/0/3
Binary file test-data/coins.ome.zarr/0/1/0/0/0/0/3 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/1/0
Binary file test-data/coins.ome.zarr/0/1/0/0/0/1/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/1/1
Binary file test-data/coins.ome.zarr/0/1/0/0/0/1/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/1/2
Binary file test-data/coins.ome.zarr/0/1/0/0/0/1/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/1/3
Binary file test-data/coins.ome.zarr/0/1/0/0/0/1/3 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/2/0
Binary file test-data/coins.ome.zarr/0/1/0/0/0/2/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/2/1
Binary file test-data/coins.ome.zarr/0/1/0/0/0/2/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/2/2
Binary file test-data/coins.ome.zarr/0/1/0/0/0/2/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/1/0/0/0/2/3
Binary file test-data/coins.ome.zarr/0/1/0/0/0/2/3 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/2/.zarray
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/2/0/0/0/0/0
Binary file test-data/coins.ome.zarr/0/2/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/2/0/0/0/0/1
Binary file test-data/coins.ome.zarr/0/2/0/0/0/0/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/2/0/0/0/1/0
Binary file test-data/coins.ome.zarr/0/2/0/0/0/1/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/0/2/0/0/0/1/1
Binary file test-data/coins.ome.zarr/0/2/0/0/0/1/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/OME/.zattrs
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/OME/.zgroup
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.ome.zarr/OME/METADATA.ome.xml
--- /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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/coins.png
Binary file test-data/coins.png has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.jpg
Binary file test-data/rocket.jpg has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/.zattrs
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/.zgroup
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/.zattrs
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/.zgroup
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/0/.zarray
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/0/0/0/0/0/0
Binary file test-data/rocket.ome.zarr/0/0/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/0/0/1/0/0/0
Binary file test-data/rocket.ome.zarr/0/0/0/1/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/0/0/2/0/0/0
Binary file test-data/rocket.ome.zarr/0/0/0/2/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/1/.zarray
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/1/0/0/0/0/0
Binary file test-data/rocket.ome.zarr/0/1/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/1/0/1/0/0/0
Binary file test-data/rocket.ome.zarr/0/1/0/1/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/1/0/2/0/0/0
Binary file test-data/rocket.ome.zarr/0/1/0/2/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/2/.zarray
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/2/0/0/0/0/0
Binary file test-data/rocket.ome.zarr/0/2/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/2/0/1/0/0/0
Binary file test-data/rocket.ome.zarr/0/2/0/1/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/0/2/0/2/0/0/0
Binary file test-data/rocket.ome.zarr/0/2/0/2/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/OME/.zattrs
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/OME/.zgroup
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/rocket.ome.zarr/OME/METADATA.ome.xml
--- 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
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/.zarray
--- 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,
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/0/0
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/0/1
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/0/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/0/2
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/0/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/1/0
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/1/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/1/1
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/1/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/1/2
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/1/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/2/0
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/2/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/2/1
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/2/1 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/2/2
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/0/2/2 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/1/0/0
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/1/0/0 has changed
diff -r 4b6c2135e547 -r b32f5368e279 test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/1/0/1
Binary file test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/0/0/1/0/1 has changed
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