Update notebook

[jburel]

Table is now created using the analysis script This PR handles new table format

Run the notebook against idr0021 on outreach

To test go to

• https://ome-lochy.openmicroscopy.org/jupyterhub-internal/hub/login
  • Enter your LDAP Credentials
  • Select snoopycrimecop/training-notebooks:master_merge_daily
  • Click Spawn
  • Select the notebook

and

cc @pwalczysko @will-moore

[pwalczysko]

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : java.lang.NoSuchMethodException: No suitable method for the given parameters
Traceback:

1. loadDataframe(project, annotationFileID, columns = c(1, 8))
2. loadDataframe(project, annotationFileID, columns = c(1, 8))
3. fac$getTableInfo(ctx, .jlong(id))
4. .jrcall(x, name, ...)
5. .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, 
 .     .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl, 
 .         "java/lang/Object"), .jnew("java/lang/String", method), 
 .     j_p, j_pc, use.true.class = TRUE, evalString = simplify, 
 .     evalArray = FALSE)
6. .jcheck(silent = FALSE)

This is done on outreach on the "old" table. Note that the table is called Summary_from_Fiji, not the batch_roi_export -> there is a mismatch there, how do we want to solve this ? (the previous script used to produce batch_roi_export tables, the present Fiji script produces Summary_from_Fiji and the name is hardcoded in this playbook

[pwalczysko]

Error in `$<-.data.frame`(`*tmp*`, "Image", value = character(0)): replacement has 0 rows, data has 405
Traceback:

1. `$<-`(`*tmp*`, "Image", value = character(0))
2. `$<-.data.frame`(`*tmp*`, "Image", value = character(0))
3. stop(sprintf(ngettext(N, "replacement has %d row, data has %d", 
 .     "replacement has %d rows, data has %d"), N, nrows), domain = NA)

the table has a different nuber of rows ?

[will-moore]

Need to use different table name

tableName <- 'Summary_from_Fiji'

and to get different columns:

# Load the table: column 14, 15 & 16 Dataset, Bounding_Box & Image) directly as R dataframe
df <- loadDataframe(project, annotationFileID, columns=c(14,15,16))

[jburel]

I am about to push a fix

[will-moore]

It works fine for me with those 2 changes

[pwalczysko]

This all looks fine here.

Maybe the only question is:

On the y-axis of the produced plot, there is estimated toroid/ring diameter - but the numbers in the graph are pure bounding box -> maybe this is intentional, ie. very rough estimate, or is it a remnant of previous naming ?

[jburel]

@pwalczysko your comment above is fixed in 20d5404 but that was not included in the version you tested

[pwalczysko]

Okay, https://github.com/ome/training-notebooks/commit/20d5404496c638280bb3af0723dcf2baf033bdc6 looks good.