Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Include annotation element bounding boxes in plottable data #1575

Merged
merged 1 commit into from
Jul 15, 2024
Merged

Include annotation element bounding boxes in plottable data #1575

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

### Improvements

- Improve plottable data endpoint to better fetch adjacent items ([#1573](../../pull/1573))
- Improve plottable data endpoint to better fetch adjacent items and annotations ([#1573](../../pull/1573), [#1574](../../pull/1574))), [#1575](../../pull/1575)))

## 1.29.2

Expand Down
8 changes: 7 additions & 1 deletion girder_annotation/girder_large_image_annotation/models/annotationelement.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -159,7 +159,7 @@ def getElements(self, annotation, region=None):
annotation['annotation']['elements'] = list(self.yieldElements(
annotation, region, annotation['_elementQuery']))

def yieldElements(self, annotation, region=None, info=None): # noqa
def yieldElements(self, annotation, region=None, info=None, bbox=False): # noqa
"""
Given an annotation, fetch the elements from the database.

Expand Down Expand Up @@ -202,6 +202,7 @@ def yieldElements(self, annotation, region=None, info=None): # noqa
maxDetails (as specified by the region dictionary), details (sum of
details returned), limit (as specified by region), centroids (a
boolean based on the region specification).
:param bbox: if True, always return bounding box information.
:returns: a list of elements. If centroids were requested, each entry
is a list with str(id), x, y, size. Otherwise, each entry is the
element record.
Expand Down Expand Up @@ -255,6 +256,9 @@ def yieldElements(self, annotation, region=None, info=None): # noqa
elif region.get('bbox'):
fields.pop('bbox.details')
fields['bbox'] = True
if bbox:
fields.pop('bbox.details', None)
fields['bbox'] = True
elementCursor = self.find(
query=query, sort=[(sortkey, sortdir)], limit=queryLimit,
offset=offset, fields=fields)
Expand Down Expand Up @@ -328,6 +332,8 @@ def yieldElements(self, annotation, region=None, info=None): # noqa
info['bbox'].get(lkey, entry['bbox'][lkey]), entry['bbox'][lkey])
info['bbox'][hkey] = max(
info['bbox'].get(hkey, entry['bbox'][hkey]), entry['bbox'][hkey])
elif bbox and 'bbox' in entry:
element['_bbox'] = entry['bbox']
yield element
details += entry.get('bbox', {}).get('details', 1)
count += 1
Expand Down
2 changes: 1 addition & 1 deletion girder_annotation/girder_large_image_annotation/rest/annotation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -633,7 +633,7 @@ def deleteItemAnnotations(self, item):
def getItemPlottableElements(self, item, annotations):
user = self.getCurrentUser()
data = utils.PlottableItemData(user, item, annotations=annotations)
return data.columns
return [col for col in data.columns if col.get('count')]

@autoDescribeRoute(
Description('Get plottable data related to an item and its annotations.')
Expand Down
178 changes: 144 additions & 34 deletions girder_annotation/girder_large_image_annotation/utils/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import itertools
import json
import math
import re
Expand Down Expand Up @@ -418,23 +419,25 @@ def _findAnnotations(self, annotations):
self.annotations.append(annotList)

def _addColumn(self, columns, fullkey, title, root, key, source):
# Root should probably only be part of this at folder/csv level
distinct = [source] if source not in {'folder'} else [source, root]
if fullkey not in columns:
columns[fullkey] = {
'key': fullkey,
'type': 'number',
'where': [[root, key, source]], 'title': title,
'where': [[distinct, key]], 'title': title,
'count': 0, 'distinct': set(), 'min': None,
'max': None}
return (root, source, 0)
return (tuple(distinct), 0)
elif [root, key, source] not in columns[fullkey]['where']:
columns[fullkey]['where'].append([root, key, source])
columns[fullkey]['where'].append([distinct, key])
where = -1
for colwhere in columns[fullkey]['where']:
if colwhere[0] == root and colwhere[2] == source:
if tuple(colwhere[0]) == tuple(distinct):
where += 1
if tuple(colwhere) == (root, key, source):
return (root, source, where)
return (root, source, where)
if colwhere[1] == key:
return (tuple(distinct), where)
return (tuple(distinct), where)

def _columnKey(self, source, root, key):
if not hasattr(self, '_columnKeyCache'):
Expand All @@ -443,7 +446,7 @@ def _columnKey(self, source, root, key):
if hashkey in self._columnKeyCache:
return self._columnKeyCache[hashkey]
fullkey = f'{root}.{key}.{source}'.lower()
title = f'{root} {key}' if root is not None else f'{key}'
title = f'{root} {key}' if root is not None and root != '' else f'{key}'
keymap = {
r'(?i)(item|image)_(id|name)$': {'key': '_0_item.name', 'title': 'Item Name'},
r'(?i)(low|min)(_|)x': {'key': '_bbox.x0', 'title': 'Bounding Box Low X'},
Expand All @@ -459,7 +462,8 @@ def _columnKey(self, source, root, key):
self._columnKeyCache[hashkey] = fullkey, title
return fullkey, title

def _scanColumnByKey(self, result, key, entry, where=0, auxidx=0, auxidx2=0, item=None):
def _scanColumnByKey(self, result, key, entry, where=0, auxidx=0,
auxidx2=0, item=None, annotation=None):
if result['type'] == 'number':
try:
[float(record[key]) for record in entry
Expand All @@ -483,17 +487,26 @@ def _scanColumnByKey(self, result, key, entry, where=0, auxidx=0, auxidx2=0, ite
if self._datacolumns and result['key'] in self._datacolumns:
self._datacolumns[result['key']][(where, (auxidx, auxidx2, ridx))] = v
if item is not None:
self._datacolumns['_0_item.name'][
self._datacolumns.get('_0_item.name', {})[
(where, (auxidx, auxidx2, ridx))] = item['name']
self._datacolumns['_2_item.id'][
self._datacolumns.get('_2_item.id', {})[
(where, (auxidx, auxidx2, ridx))] = str(item['_id'])

def _scanColumn(self, meta, source, columns, auxmeta=None, auxidx2=0, items=None):
if annotation is not None:
self._datacolumns.get('_1_annotation.name', {})[
(where, (auxidx, auxidx2, ridx))] = annotation.get(
'annotation', {}).get('name')
self._datacolumns.get('_3_annotation.id', {})[
(where, (auxidx, auxidx2, ridx))] = str(annotation['_id'])
self._datacolumns.get('_4_annotation.description', {})[
(where, (auxidx, auxidx2, ridx))] = annotation.get(
'annotation', {}).get('description')

def _scanColumn(self, meta, source, columns, auxmeta=None, auxidx2=0,
items=None, annotations=None):
for root, entry in (list(meta.items()) + [(None, [meta])]):
if not isinstance(entry, list) or not len(entry) or not isinstance(entry[0], dict):
continue
for key in entry[0]:
print(key)
if not isinstance(entry[0][key], self.allowedTypes):
continue
fullkey, title = self._columnKey(source, root, key)
Expand All @@ -502,22 +515,112 @@ def _scanColumn(self, meta, source, columns, auxmeta=None, auxidx2=0, items=None
result = columns[fullkey]
self._scanColumnByKey(
result, key, entry, where, 0, auxidx2,
items[0] if items and len(items) > 0 else None)
items[0] if items and len(items) > 0 else None,
annotations[0] if annotations and len(annotations) > 0 else None)
if auxmeta:
for auxidx, aux in enumerate(auxmeta):
if root is None:
if isinstance(aux, dict) and key in aux:
self._scanColumnByKey(
result, key, [aux], where, auxidx + 1, auxidx2,
items[auxidx + 1] if items and len(items) > auxidx + 1 else
None,
annotations[auxidx + 1]
if annotations and len(annotations) > auxidx + 1 else
None)
elif (isinstance(aux.get(root), list) and
len(aux[root]) and
isinstance(aux[root][0], dict) and
key in aux[root][0]):
self._scanColumnByKey(
result, key, aux[root], where, auxidx + 1, auxidx2,
items[auxidx + 1] if items and len(items) > auxidx + 1 else None)
items[auxidx + 1] if items and len(items) > auxidx + 1 else None,
annotations[auxidx + 1] if annotations and
len(annotations) > auxidx + 1 else None)

def _scanElementColumns(self, source, columns, elems, auxidx, items, annotations, keys):
rows = {}
for ridx, elem in enumerate(elems):
if auxidx < len(items) and items[auxidx]:
rows.setdefault('_0_item.name', []).append(items[auxidx]['name'])
rows.setdefault('_2_item.id', []).append(str(items[auxidx]['_id']))
if auxidx < len(annotations) and annotations[auxidx]:
rows.setdefault('_1_annotation.name', []).append(
annotations[auxidx].get('annotation', {}).get('name'))
rows.setdefault('_3_annotation.id', []).append(str(annotations[auxidx]['_id']))
rows.setdefault('_4_annotation.description', []).append(
annotations[auxidx].get('annotation', {}).get('description'))
if '_bbox' in elem:
rows.setdefault('_bbox.x0', []).append(elem['_bbox']['lowx'])
rows.setdefault('_bbox.y0', []).append(elem['_bbox']['lowy'])
rows.setdefault('_bbox.x1', []).append(elem['_bbox']['highx'])
rows.setdefault('_bbox.y1', []).append(elem['_bbox']['highy'])
# TODO: Add group and label
if not auxidx and not ridx and 'user' in elem:
for key, entry in elem['user'].items():
if not isinstance(entry, self.allowedTypes):
continue
root = ''
fullkey, title = self._columnKey(source, root, key)
colwhere = self._addColumn(
columns, fullkey, title, root, key, source)
keys[key] = (fullkey, colwhere)
# TODO: Populate group and label
for key, (fullkey, _keywhere) in keys.items():
entry = elem.get('user', {}).get(key)
if not isinstance(entry, self.allowedTypes):
entry = None
rows.setdefault(fullkey, []).append(entry)
return rows

def _scanElements(self, elements, source, columns, auxidx2, items, annotations):
where = self._addColumn(
columns, '_0_item.name', 'Item Name', '', 'name', 'annotationelement')
self._addColumn(
columns, '_2_item.id', 'Item ID', '', '_id', 'annotationelement')
self._addColumn(
columns, '_1_annotation.name', 'Annotation Name', '', 'name', 'annotationelement')
self._addColumn(
columns, '_3_annotation.id', 'Annotation ID', '', '_id', 'annotationelement')
self._addColumn(
columns, '_4_annotation.description', 'Annotation Description', '',
'description', 'annotationelement')
self._addColumn(
columns, '_bbox.x0', 'Bounding Box Low X', '', 'lowx', 'annotationelement')
self._addColumn(
columns, '_bbox.y0', 'Bounding Box Low Y', '', 'lowy', 'annotationelement')
self._addColumn(
columns, '_bbox.x1', 'Bounding Box High X', '', 'highx', 'annotationelement')
self._addColumn(
columns, '_bbox.y1', 'Bounding Box High Y', '', 'highy', 'annotationelement')
keys = {}
for auxidx, elems in enumerate(elements):
if not elems:
continue
rows = self._scanElementColumns(
source, columns, elems, auxidx, items, annotations, keys)
for fullkey, entry in rows.items():
result = columns[fullkey]
if result['type'] == 'number':
try:
[float(v) for v in entry if isinstance(v, self.allowedTypes)]
except Exception:
result['type'] = 'string'
result['distinct'] = {str(v) for v in result['distinct']}
for ridx, v in enumerate(entry):
if not isinstance(v, self.allowedTypes):
continue
result['count'] += 1
v = float(v) if result['type'] == 'number' else str(v)
if len(result['distinct']) <= self.maxDistinct:
result['distinct'].add(v)
if result['type'] == 'number':
if result['min'] is None:
result['min'] = result['max'] = v
result['min'] = min(result['min'], v)
result['max'] = max(result['max'], v)
if self._datacolumns and fullkey in self._datacolumns:
self._datacolumns[fullkey][(where, (auxidx, auxidx2, ridx))] = v

@property
def columns(self):
Expand All @@ -541,6 +644,8 @@ def columns(self):

:returns: a sorted list of data entries.
"""
from ..models.annotationelement import Annotationelement

if self._columns is not None:
return self._columns
columns = {}
Expand All @@ -555,10 +660,12 @@ def columns(self):
for anidx, annot in enumerate(self.annotations[0] if self.annotations is not None else []):
self._scanColumn(
annot.get('annotation', {}).get('attributes', {}),
'annotation', columns, None, anidx,
[itemannot[anidx].get('annotaiton').get('attributes', {})
'annotation', columns,
[itemannot[anidx].get('annotation').get('attributes', {})
for itemannot in self.annotations[1:]
if itemannot[anidx] is not None])
if itemannot[anidx] is not None],
anidx, items=self.items,
annotations=[a[anidx] for a in self.annotations])
if not anidx:
self._addColumn(
columns, '_1_annotation.name', 'Annotation Name',
Expand All @@ -567,18 +674,20 @@ def columns(self):
columns, '_3_annotation.id', 'Annotation ID',
'Annotation', '_id', 'base')
self._addColumn(
columns, '_bbox.x0', 'Bounding Box Low X', 'bbox', 'lowx',
'annotationelement')
self._addColumn(
columns, '_bbox.y0', 'Bounding Box Low Y', 'bbox', 'lowy',
'annotationelement')
self._addColumn(
columns, '_bbox.x1', 'Bounding Box High X', 'bbox',
'highx', 'annotationelement')
self._addColumn(
columns, '_bbox.y1', 'Bounding Box High Y', 'bbox',
'highy', 'annotationelement')
# TODO: add annotation elements
columns, '_4_annotation.description', 'Annotation Description',
'Annotation', 'description', 'base')
# add annotation elements
firstelem = next(Annotationelement().yieldElements(annot), None)
if firstelem is not None:
self._scanElements(
[list(itertools.islice(
Annotationelement().yieldElements(a[anidx], bbox=True), 10000))
if a[anidx] else None for a in self.annotations],
'annotationelement', columns,
anidx,
items=self.items,
annotations=[a[anidx] for a in self.annotations],
)
# TODO: Add csv
for result in columns.values():
if len(result['distinct']) <= self.maxDistinct:
Expand Down Expand Up @@ -612,7 +721,8 @@ def data(self, columns, requiredColumns=None):
collist = self.columns
for coldata in self._datacolumns.values():
rows |= set(coldata.keys())
rows = sorted(rows)
rows = sorted(rows, key=lambda row: (
tuple(x if x is not None else '' for x in row[0]), row[1]))
colsout = [col.copy() for col in collist if col['key'] in columns]
for cidx, col in enumerate(colsout):
col['index'] = cidx
Expand All @@ -635,9 +745,9 @@ def data(self, columns, requiredColumns=None):
# Refresh our count, distinct, distinctcount, min, max for each column
for cidx, col in enumerate(colsout):
col['count'] = len([row[cidx] for row in data if row[cidx] is not None])
if col['type'] == 'number':
if col['type'] == 'number' and col['count']:
col['min'] = min(row[cidx] for row in data if row[cidx] is not None)
col['max'] = min(row[cidx] for row in data if row[cidx] is not None)
col['max'] = max(row[cidx] for row in data if row[cidx] is not None)
distinct = {str(row[cidx]) for row in data if row[cidx] is not None}
if len(distinct) <= self.maxDistinct:
col['distinct'] = sorted(distinct)
Expand Down