Protocol editor: ROI & folder loop

[Arthur Bellier]

two part question:

In the Protocol editor, following the Crop sequence to ROI block, are we supposed to use an indexer, an iterator or something else?

Also when using a folder loop, even with a clean folder containing only tiff, verified to be open-able by ICY, I get a error message reading:

- Error in block "Files to sequence (#1)":
unable to read files (java.io.File cannot be cast to [Ljava.io.File;)

This message is repeated one time per .tif file

[Alexandre Dufour]

Hi Arthur,

On 30 mai 2013, at 11:07, Arthur Bellier wrote:

two part question:

In the Protocol editor, following the Crop sequence to ROI block, are we supposed to use an indexer, an iterator or something else?

An indexer would be if you have only one crop (so one ROI). If you have more than one, you would use an "Array Loop" on the list of crops.

Also when using a folder loop, even with a clean folder containing only tiff, verified to be open-able by ICY, I get a error message reading:

- Error in block "Files to sequence (#1)":
unable to read files (java.io.File cannot be cast to [Ljava.io.File;)

This message is repeated one time per .tif file

Indeed, because you are using the "Files to sequence" (with an "s") and not "File to sequence" (with no "s"). The difference is that the former opens multiple images into one sequence, while the latter opens each file into its on sequence (which is what you want here).

Let me know if this helps,

Alexandre

[Arthur Bellier]

Thanks.

I hadn't understood the difference between singular and plural in blocks.

Also I only have 1 ROI so an Indexer works ...
...except it crops the image to the smallest rectangle containing all or my ROI, not to my ROI.

To get things done outside of the protocol editor I inverted my ROI and then filled my ROI with a color. Unfortunately I haven't found how to do this ( or anything that allows me to apply modification to a non-rectangular ROI ) in Protocols.

Arthur

[Arthur Bellier]

Do you have an example sequence for running any block on a non-rectangular ROI ? I can't seen to find how to do this.

Arthur

[Alexandre Dufour]

On 31 mai 2013, at 12:14, Arthur Bellier wrote:

Do you have an example sequence for running any block on a non-rectangular ROI ? I can't seen to find how to do this.

What do you mean by this? There is no distinction between types of ROI in protocols, so any block taking ROI as input should work properly. Which block did you have in mind?

Alexandre

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[Arthur Bellier]

Well with this protocol and image+ROI, the output displayed by block 4 is the original image file, just cropped to the smallest possible rectangle containing the ROI, not just the ROI.

[Arthur Bellier]

sorry, display has to come from "element" of block 4, I have updated the protocol