Headless and batch modes

kjamartens commented 8 months ago

Hi Florian, Wonderful work on PoCA!

I want to know if it could be possible to run PoCA 'headless' and/or in 'batch' fashion. My main goal, for instance, would be similar to the following:

Loop over all files (possibly matching a certain Regex or extension or so) in a certain folder
Run a macro in PoCA (including opening that file) on each file, and e.g. store the objectlist (the locsObjs.csv) in an adjacent folder, with name of the file that reflects the original file name
Rinse and repeat

Importantly, these might be somewhat giant files, and I don't want to interact with them, but just use PoCA as a batch analysis method. I assume that not requiring visualisation might help a lot with performance?

Please let me know if there is anything you can do in this aspect

Best, Koen Martens

flevet commented 8 months ago

Hi Koen,

Batch processing a folder in PoCA is possible even if it is the most intuitive feature... ^^' Nevertheless, until version 0.9.0 (just pushed now), it was not possible to save one object stat file per dataset. This is changed now.

The following macro allows to open a file (in a specific way with the columns), create a delaunay, do a segmentation, save the objec stats and close the dataset:

{
    "MainWindow": {
        "open": {
            "calibration_t": 1.0,
            "calibration_xy": 1.0,
            "calibration_z": 1.0,
            "frame": 4,
            "intensity": 3,
            "separator": 44,
            "sigmaZ": 6,
            "x": 0,
            "y": 1,
            "z": 2
        }
    }
}
{
    "DetectionSet": {
        "computeDelaunay": {
            "onSphere": false
        }
    }
}
{
    "DelaunayTriangulation": {
        "objectCreationParameters": {
            "cutDistance": 50.0,
            "inROIs": false,
            "maxArea": 1000.0,
            "maxLocs": 500,
            "minArea": 0.0,
            "minLocs": 3,
            "useDistance": true,
            "useMaxArea": false,
            "useMaxLocs": false,
            "useMinArea": false,
            "useMinLocs": true
        }
    }
}
{
    "DelaunayTriangulation": {
        "createFilteredObjects": ""
    }
}
{
    "DelaunayTriangulation": {
        "selected": false
    }
}
{
    "ObjectList": {
        "saveStatsObjs": {
            "separator": ","
        }
    }
}
{
    "MainWindow": {
        "close": ""
    }
}

When this macro is loaded in the Runner of theMacro tab, you can click the Open dir button and choose a folder to batch process.

macro_folder

The macro will be applied on all the files inside the folder. If one file is called example1.csv, the object stat file created will be called example1_statsObjs.csv.

v0.9.0 is here: https://github.com/flevet/PoCA/releases/tag/0.9.0

Let me know if everything works.

flevet commented 3 months ago

Closing the issue as there was no follow-up

flevet / PoCA

Headless and batch modes #5