2D array with different number of elements

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Is it possible to have this array in VHDL?

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No.

You could use an array if you changed your format

[i][j] =

[1][numvalid, sample1, sample2, sample3, 0 , 0 ]

[2][numvalid, sample1, sample2, sample3, sample4, sample5]

[3][numvalid, sample1, sample2, 0 , 0 , 0 ]

or you can use a list of lists (or an array of lists).

You'll have to be careful if you're using this for synthesis though.

Cheers,

Dave