will-moore
commented
1 year ago Using --max_workers=1 doesn't seem to make a difference:
$ bioformats2raw WB.xml 9846152_mw1.zarr --max_workers=1 --debug > bf2raw_mw1.log
OpenJDK 64-Bit Server VM warning: You have loaded library /tmp/opencv_openpnp1435327528824061833/nu/pattern/opencv/linux/x86_64/libopencv_java342.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c <libfile>', or link it with '-z noexecstack'.
Killed
$ find 9846152_mw1.zarr/ -type f | wc -l
18211
melissalinkert
sbesson
jburel
I'm trying to convert https://idr.openmicroscopy.org/webclient/?show=image-9846152 (requested at https://forum.image.sc/t/converting-other-idr-images-into-public-zarr/44025/13) to OME-NGFF.
Working on
pilot-zarr1-devI have downloaded the files to/data/idr0048withChecked that the downloaded files match what's on IDR:
Running in a terminal screen, I see:
The 3 times I have tried this, I get about the same number of files generated:
$ cat 9846152.zarr/.zattrs
``` { "bioformats2raw.layout" : 3 }(base) [wmoore@pilot-zarr1-dev idr0048]$ cat 9846152.zarr/0/.zattrs { "multiscales" : [ { "metadata" : { "method" : "loci.common.image.SimpleImageScaler", "version" : "Bio-Formats 6.10.1" }, "axes" : [ { "name" : "t", "type" : "time" }, { "name" : "c", "type" : "channel" }, { "unit" : "pixel", "name" : "z", "type" : "space" }, { "unit" : "pixel", "name" : "y", "type" : "space" }, { "unit" : "pixel", "name" : "x", "type" : "space" } ], "name" : "P_t00000, W_s00_0", "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" } ] }, { "path" : "3", "coordinateTransformations" : [ { "scale" : [ 1.0, 1.0, 1.0, 8.0, 8.0 ], "type" : "scale" } ] }, { "path" : "4", "coordinateTransformations" : [ { "scale" : [ 1.0, 1.0, 1.0, 16.0, 16.0 ], "type" : "scale" } ] }, { "path" : "5", "coordinateTransformations" : [ { "scale" : [ 1.0, 1.0, 1.0, 32.0, 32.0 ], "type" : "scale" } ] }, { "path" : "6", "coordinateTransformations" : [ { "scale" : [ 1.0, 1.0, 1.0, 64.0, 64.0 ], "type" : "scale" } ] }, { "path" : "7", "coordinateTransformations" : [ { "scale" : [ 1.0, 1.0, 1.0, 128.0, 128.0 ], "type" : "scale" } ] } ], "version" : "0.4" } ], "omero" : { "channels" : [ { "color" : "FF0000", "coefficient" : 1, "active" : true, "label" : "Channel 0", "window" : { "min" : 0.0, "max" : 65535.0, "start" : 0.0, "end" : 65535.0 }, "family" : "linear", "inverted" : false }, { "color" : "00FF00", "coefficient" : 1, "active" : true, "label" : "Channel 1", "window" : { "min" : 0.0, "max" : 65535.0, "start" : 0.0, "end" : 65535.0 }, "family" : "linear", "inverted" : false }, { "color" : "0000FF", "coefficient" : 1, "active" : true, "label" : "Channel 2", "window" : { "min" : 0.0, "max" : 65535.0, "start" : 0.0, "end" : 65535.0 }, "family" : "linear", "inverted" : false } ], "rdefs" : { "defaultT" : 0, "model" : "color", "defaultZ" : 45 } } } ```but only the highest resolution directory exists (and looks incomplete):
The log file looks like this (middle repeated section not included):
bf2raw.log
``` 2023-01-17 13:16:21,753 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.in.URLReader java.lang.ClassNotFoundException: loci.formats.in.URLReader at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:264) at loci.formats.ClassList.parseLine(ClassList.java:196) at loci.formats.ClassList.parseFile(ClassList.java:258) at loci.formats.ClassList.