Closed jburel closed 6 years ago
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$getTableInfo(ctx, .jlong(id))
4. .jrcall(x, name, ...)
5. .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,
. .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl,
. "java/lang/Object"), .jnew("java/lang/String", method),
. j_p, j_pc, use.true.class = TRUE, evalString = simplify,
. evalArray = FALSE)
6. .jcheck(silent = FALSE)
This is done on outreach on the "old" table. Note that the table is called Summary_from_Fiji
, not the batch_roi_export
-> there is a mismatch there, how do we want to solve this ? (the previous script used to produce batch_roi_export
tables, the present Fiji script produces Summary_from_Fiji
and the name is hardcoded in this playbook
Error in `$<-.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 ?
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))
I am about to push a fix
It works fine for me with those 2 changes
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 ?
@pwalczysko your comment above is fixed in 20d5404 but that was not included in the version you tested
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
and
cc @pwalczysko @will-moore