Duplicate points and bounding box in PyQGIS?

Question

I am trying to find all points in a vector layer that do not have a duplicate point.

To do this, for each point I create a list of features that intersect its bounding box ('candidates') then check if any candidate is an exact geometry match. I've included the exact code below.

However, no matter how I tweak the code I don't end up with any duplicate points. I know for a fact there are many duplicate points (various topology checks and knowledge of dataset) so there's something wrong.

Is this an issue with using the bounding box, or another part of my code?

I'm using Python because every existing tool I've found only flags duplicates, but tool suggestions are fine too.

Working with QGIS 3.4x64 and Python 3.7 on Windows 10.

geoms = {} # { vertex id : geom }

for v in point_layer.getFeatures():
    if not v.hasGeometry():
        continue

    geoms[v.id()] = v.geometry() 

index = QgsSpatialIndex()
no_dup = [] #list of vertex IDs with no duplicates 
    for v_id, geometry in geoms.items():
    candidates = index.intersects(geometry.boundingBox()) 
    duplicates = [] 

    for candidate_id in candidates:
        if geometry.isGeosEqual(geoms[candidate_id]):
            duplicates.append(v_id)

    if len(duplicates) == 1: #only one point in location
        no_dup.append(v_id)

Note: I considered creating a buffer instead of using the boundary box but I have over 100k features and would prefer not to create another layer

Answer 1

Solved: I hadn't populated the QgsSpatialIndex properly.

index = QgsSpatialIndex()
geoms = {} # { vertex id : geom }
for v in point_layer.getFeatures():
    if not v.hasGeometry():
        continue

    geoms[v.id()] = v.geometry() #pop vertex geoms dict
    index.addFeature(v)

Answer 2

You could use equals() :

geoms = {}

point_layer = iface.activeLayer()
for v in point_layer.getFeatures():
    if not v.hasGeometry():
        continue
    geoms[v.id()] = v.geometry() 

no_dup = []
for v_id1, geom1 in geoms.items():
    i = 0
    for v_id2, geom2 in geoms.items():
        if v_id1 != v_id2 and geom1.equals(geom2):
            i += 1
    if i == 0:
        no_dup.append(v_id)

print('nb {}'.format(len(no_dup)))

See How to check if two qgsPoints are equal in PyQgis