Automated export of maps?

JakubS

Hi all,

Apologies if this has been addressed in an earlier thread--I couldn't find anything on the forum, but if I missed something, I would appreciate a pointer in the right direction.

I'm trying to batch-export and process dozens of maps, and would like to:

(1) Find a way to apply the upper and lower limits for all elements for all samples [currently, I'm able to set, e.g., percentile-based limits on all maps within a single sample, but when I navigate to a new sample in the Imaging tab, the limits are reset)

(2) Export maps for all samples (pdf or similar) using the same output channels, preferably with scale bars and color bars.

Is there a python-based script that anyone in the community has developed that helps with this? Or a function in iolite that I'm missing?

Many thanks in advance!

Jakub

Joe

JakubS

I couldn't think of a way to do this for the current release. I've just added some functions to the python API and in the next release, you should be able to do this with something like:

from iolite.QtGui import QFileDialog

path = QFileDialog.getExistingDirectory()

if not path:
    raise RuntimeError('No path provided')

groups = [g.name for g in data.selectionGroupList(data.Sample | data.ReferenceMaterial)]
channels = [c.name for c in data.timeSeriesList(data.Input)]

for group in groups:
    imaging.setGroup(group)
    imaging.setChannels(channels)

    for channel in channels:
        image = imaging.image(channel)
        # Customize how you want to set limits...
        image.setLowerLimitType('Value')
        image.setUpperLimitType('Value')
        image.setLimits(0, 1000) 

        plot = image.createPlot(True, True) # With color scale and length scale
        plot.savePdf(f'{path}/{group} - {channel}.pdf')

The update should come out this week.

Note that this will only give you the individual images. I'll add it to the longer term todo to be able to run the normal export via python so that you could also export matrices, overview, ROI, etc.

All the best,