How to count points within the current Print composer atlas feature in QGIS 2.8?

This works for me: use the aggregate() expression in a text label, with within($geometry,@atlas_geometry) as a filter for points within your atlas feature.

The full syntax in your text label would be

[% aggregate('LAYER_NAME','count',"UNIQUE_NON_NULL_ATTRIBUTE_FOR_COUNTING",within($geometry,@atlas_geometry)) %]

That will count all the points in your specified layer - by an unique non-null attribute, so each point is distinct - but only if the point geometry is within the atlas geometry.

The [% %] is required to make the expression work. And note the quotation marks - you must use double quotes for the attribute name.

As a bonus you can add further filters, so to address one of the comments above, you can modify the filter to say within($geometry,@atlas_geometry) AND "village" = 'A', or whatever combination.

I haven't extensively tested this out, especially on large/complex datasets, but it seems to do the job.

You need to create a script counting point within the current atlas geometry.

In the expression function editor add this code:

from qgis.core import *
from qgis.gui import *
from qgis.utils import iface

@qgsfunction(args="auto", group='Custom')
def countPointsInCurrentAltlasFeature(pointLayerName, geomAtlas, feature, parent):
    # If point geom is empty, return 0
    if (geomAtlas is None):
        return 0

    # Get point layer reference from layername
    pointLayer = QgsMapLayerRegistry.instance().mapLayersByName(pointLayerName)[0]

    # Raise if layer not found
    if pointLayer is None:
        raise Exception("Layer not found: " + pointLayerName)

    # Count point within current Atlas feature
    countPoint = 0
    for pointFeature in pointLayer.getFeatures():
        pointGeom = pointFeature.geometry()
        if (pointGeom is None):
            continue
        if pointGeom.within(geomAtlas):
            countPoint += 1

    return countPoint

Use the new function as an expression for a Print Composer label like:

Villages in province: [% countPointsInCurrentAltlasFeature( 'Villages', $atlasgeometry)%]