def show_helpmsg(co_wgt):
msg = ut.textblock("""
This step is for synchronizing the time of the images being imported
with the actual time of the imageset.
Use the Previous and Next buttons until the 'Time Synchronization Picture' is of the clock
taken at the beginning of the imageset.
Once found, change the date and time in the boxes below to match the time of the clock in
the image, and correct the date if necessary.
Once done, click 'Set' and the difference will be applied to all images currently
being imported. If you are sure the camera was synchronized, you
can skip this step by pressing 'Skip'.
""")
gt.user_info(co_wgt, msg=msg, title='Time Sync Help')
def show_helpmsg(co_wgt):
msg = ut.textblock(
"""
This step is for synchronizing the time of the images being imported
with the actual time of the imageset.
Use the Previous and Next buttons until the 'Time Synchronization Picture' is of the clock
taken at the beginning of the imageset.
Once found, change the date and time in the boxes below to match the time of the clock in
the image, and correct the date if necessary.
Once done, click 'Set' and the difference will be applied to all images currently
being imported. If you are sure the camera was synchronized, you
can skip this step by pressing 'Skip'.
""")
guitool.user_info(co_wgt, msg=msg, title='Time Sync Help')
def define_flann_bindings(binding_name):
"""
Define the binding names for flann
"""
# default c source
c_source = None
optional_args = None
c_source_part = None
py_source = None
py_alias = None
py_args = None
pydoc = None
cpp_param_doc = {
'cols':
'number of columns in the dataset (feature dimensionality)',
'dataset':
'pointer to a data set stored in row major order',
'dists':
ut.packtext(
'''pointer to matrix for the distances of the nearest neighbors of
the testset features in the dataset'''),
'flann_params':
'generic flann parameters',
'index_ptr':
'the index (constructed previously using flann_build_index)',
'nn':
'how many nearest neighbors to return',
'rebuild_threshold':
ut.packtext(
'''reallocs index when it grows by factor of `rebuild_threshold`.
A smaller value results is more space efficient but less
computationally efficient. Must be greater than 1.'''),
'result_ids':
ut.packtext(
'''pointer to matrix for the indices of the nearest neighbors of
the testset features in the dataset (must have tcount number of
rows and nn number of columns)'''),
'rows':
'number of rows (features) in the dataset',
'tcount':
ut.packtext('''number of rows (features) in the query dataset (same
dimensionality as features in the dataset)'''),
'testset':
'pointer to a query set stored in row major order',
'level':
'verbosity level'
}
standard_csource = ut.codeblock(r'''
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
return index->{cpp_binding_name}();
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
throw;
}}
''')
return_doc = None
cpp_binding_name = binding_name
zero_success = 'zero or a number <0 for error'
if binding_name == 'clean_removed_points':
cpp_binding_name = ut.to_camel_case(binding_name)
return_type = 'void'
docstr = 'Deletes removed points in index?'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'veclen':
return_type = 'int'
docstr = 'Returns number of features in this index'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'size':
return_type = 'int'
docstr = 'returns The dimensionality of the features in this index.'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'getType':
return_type = 'flann_algorithm_t'
docstr = 'returns The index type (kdtree, kmeans,...)'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'used_memory':
docstr = ut.codeblock('''
Returns the amount of memory (in bytes) used by the index
index_ptr = pointer to pre-built index.
Returns: int
''')
c_source = ut.codeblock(r'''
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
return index->usedMemory();
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
''')
py_source = ut.codeblock('''
if self.__curindex is None:
return 0
return flann.used_memory[self.__curindex_type](self.__curindex)
''')
binding_argnames = ['index_ptr']
return_type = 'int'
elif binding_name == 'add_points':
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<ElementType> points = Matrix<ElementType>(points, rows, index->veclen());
index->addPoints(points, rebuild_threshold);
return 0;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
''')
py_source = ut.codeblock('''
if new_pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % new_pts.dtype)
if new_pts.dtype != self.__curindex_type:
raise FLANNException('New points must have the same type')
new_pts = ensure_2d_array(new_pts, default_flags)
rows = new_pts.shape[0]
flann.add_points[self.__curindex_type](self.__curindex, new_pts, rows, rebuild_threshold)
return self.__added_data.append(new_pts)
''')
#return_type = 'void'
return_type = 'int'
docstr = 'Adds points to pre-built index.'
if False:
binding_argnames = [
'index_ptr',
'points',
'rows',
'cols', # TODO: can remove
'rebuild_threshold',
]
else:
binding_argnames = [
'index_ptr',
'points',
'rows',
'rebuild_threshold',
]
return_doc = '0 if success otherwise -1'
py_args = ['new_pts', 'rebuild_threshold=2.']
cpp_param_doc['points'] = 'pointer to array of points'
elif binding_name == 'remove_point':
c_source = ut.codeblock(r'''
size_t point_id(point_id_uint);
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
index->removePoint(point_id);
return 0;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
''')
py_source = ut.codeblock('''
flann.remove_point[self.__curindex_type](self.__curindex, point_id)
self.__removed_ids.append(point_id)
''')
#return_type = 'void'
return_type = 'int'
docstr = 'Removes a point from the index'
return_doc = zero_success
cpp_param_doc['point_id'] = 'point id to be removed'
cpp_param_doc['index_ptr'] = 'The index that should be modified'
binding_argnames = ['index_ptr', 'point_id']
elif binding_name == 'remove_points':
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
try {{
if (index_ptr==NULL) {{
thow FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
index->removePoints(id_list, num);
return;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return;
}}
''')
py_source = ut.codeblock('''
id_list = np.array(id_list, dtype=np.int32)
num = len(id_list)
flann.remove_points[self.__curindex_type](self.__curindex, id_list, num)
self.__removed_ids.extend(id_list)
''')
cpp_param_doc['index_ptr'] = 'The index that should be modified'
cpp_param_doc['id_list'] = 'list of point ids to be removed'
cpp_param_doc['num'] = 'number of points in id_list'
docstr = 'Removes multiple points from the index'
return_doc = 'void'
py_args = ['id_list']
return_type = 'void'
binding_argnames = ['index_ptr', 'id_list', 'num']
elif binding_name == 'compute_cluster_centers':
docstr = ut.textblock(r'''
Clusters the features in the dataset using a hierarchical kmeans
clustering approach. This is significantly faster than using a
flat kmeans clustering for a large number of clusters.
''')
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {
init_flann_parameters(flann_params);
Matrix<ElementType> inputData(dataset,rows,cols);
KMeansIndexParams params(flann_params->branching, flann_params->iterations, flann_params->centers_init, flann_params->cb_index);
Matrix<DistanceType> centers(result_centers, clusters,cols);
int clusterNum = hierarchicalClustering<Distance>(inputData, centers, params, d);
return clusterNum;
}
catch (std::runtime_error& e) {
Logger::error("Caught exception: %s\n",e.what());
return -1;
}
'''.replace('{', '{{').replace('}', '}}'))
py_source = ut.codeblock('''
# First verify the paremeters are sensible.
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
if int(branch_size) != branch_size or branch_size < 2:
raise FLANNException('branch_size must be an integer >= 2.')
branch_size = int(branch_size)
if int(num_branches) != num_branches or num_branches < 1:
raise FLANNException('num_branches must be an integer >= 1.')
num_branches = int(num_branches)
if max_iterations is None:
max_iterations = -1
else:
max_iterations = int(max_iterations)
# init the arrays and starting values
pts = ensure_2d_array(pts, default_flags)
npts, dim = pts.shape
num_clusters = (branch_size - 1) * num_branches + 1
if pts.dtype.type == np.float64:
result = np.empty((num_clusters, dim), dtype=np.float64)
else:
result = np.empty((num_clusters, dim), dtype=np.float32)
# set all the parameters appropriately
self.__ensureRandomSeed(kwargs)
params = {'iterations': max_iterations,
'algorithm': 'kmeans',
'branching': branch_size,
'random_seed': kwargs['random_seed']}
self.__flann_parameters.update(params)
numclusters = flann.compute_cluster_centers[pts.dtype.type](
pts, npts, dim, num_clusters, result,
pointer(self.__flann_parameters))
if numclusters <= 0:
raise FLANNException('Error occured during clustering procedure.')
if dtype is None:
return result
else:
return dtype(result)
''').replace('}', '}}').replace('{', '{{')
return_doc = ut.packtext(
'''number of clusters computed or a number <0 for error. This
number can be different than the number of clusters requested, due
to the way hierarchical clusters are computed. The number of
clusters returned will be the highest number of the form
(branch_size-1)*K+1 smaller than the number of clusters
requested.''')
cpp_param_doc['clusters'] = 'number of cluster to compute'
cpp_param_doc[
'result_centers'] = 'memory buffer where the output cluster centers are stored'
cpp_param_doc[
'flann_params'] = 'generic flann parameters and index_params used to specify the kmeans tree parameters (branching factor, max number of iterations to use)'
return_type = 'int'
binding_argnames = [
'dataset', 'rows', 'cols', 'clusters', 'result_centers',
'flann_params'
]
optional_args = ['Distance d = Distance()']
py_alias = 'hierarchical_kmeans'
py_args = 'pts, branch_size, num_branches, max_iterations=None, dtype=None, **kwargs'.split(
', ')
elif binding_name == 'radius_search':
docstr = ut.codeblock(r'''
Performs an radius search using an already constructed index.
In case of radius search, instead of always returning a predetermined
number of nearest neighbours (for example the 10 nearest neighbours), the
search will return all the neighbours found within a search radius
of the query point.
The check parameter in the FLANNParameters below sets the level of approximation
for the search by only visiting "checks" number of features in the index
(the same way as for the KNN search). A lower value for checks will give
a higher search speedup at the cost of potentially not returning all the
neighbours in the specified radius.
''')
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {{
init_flann_parameters(flann_params);
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<int> m_result_ids(result_ids, 1, max_nn);
Matrix<DistanceType> m_dists(dists1d, 1, max_nn);
SearchParams search_params = create_search_params(flann_params);
int count = index->radiusSearch(Matrix<ElementType>(query1d, 1, index->veclen()),
m_result_ids,
m_dists, radius, search_params );
return count;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
''')
py_source = ut.codeblock('''
if self.__curindex is None:
raise FLANNException(
'build_index(...) method not called first or current index deleted.')
if query.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % query.dtype)
if self.__curindex_type != query.dtype.type:
raise FLANNException('Index and query must have the same type')
npts, dim = self.get_indexed_shape()
assert(query.shape[0] == dim), 'data and query must have the same dims'
result = np.empty(npts, dtype=index_type)
if self.__curindex_type == np.float64:
dists = np.empty(npts, dtype=np.float64)
else:
dists = np.empty(npts, dtype=np.float32)
self.__flann_parameters.update(kwargs)
nn = flann.radius_search[
self.__curindex_type](
self.__curindex, query, result, dists, npts, radius,
pointer(self.__flann_parameters))
return (result[0:nn], dists[0:nn])
''')
cpp_param_doc['index_ptr'] = 'the index'
cpp_param_doc['query1d'] = 'query point'
cpp_param_doc['dists1d'] = 'similar, but for storing distances'
cpp_param_doc[
'result_ids'] = 'array for storing the indices found (will be modified)'
cpp_param_doc['max_nn'] = 'size of arrays result_ids and dists1d'
cpp_param_doc[
'radius'] = 'search radius (squared radius for euclidian metric)'
return_doc = 'number of neighbors found or <0 for an error'
return_type = 'int'
binding_argnames = [
'index_ptr',
'query1d',
'result_ids',
'dists1d',
'max_nn',
'radius',
'flann_params',
]
py_alias = 'nn_radius'
py_args = 'query, radius, **kwargs'.split(', ')
elif binding_name == 'find_nearest_neighbors_index':
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {
init_flann_parameters(flann_params);
if (index_ptr==NULL) {
throw FLANNException("Invalid index");
}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<int> m_indices(result_ids,tcount, nn);
Matrix<DistanceType> m_dists(dists, tcount, nn);
SearchParams search_params = create_search_params(flann_params);
index->knnSearch(Matrix<ElementType>(testset, tcount, index->veclen()),
m_indices,
m_dists, nn, search_params );
return 0;
}
catch (std::runtime_error& e) {
Logger::error("Caught exception: %s\n",e.what());
return -1;
}
return -1;
''').replace('{', '{{').replace('}', '}}')
py_source = ut.codeblock('''
if self.__curindex is None:
raise FLANNException(
'build_index(...) method not called first or current index deleted.')
if qpts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % qpts.dtype)
if self.__curindex_type != qpts.dtype.type:
raise FLANNException('Index and query must have the same type')
qpts = ensure_2d_array(qpts, default_flags)
npts, dim = self.get_indexed_shape()
if qpts.size == dim:
qpts.reshape(1, dim)
nqpts = qpts.shape[0]
assert qpts.shape[1] == dim, 'data and query must have the same dims'
assert npts >= num_neighbors, 'more neighbors than there are points'
result = np.empty((nqpts, num_neighbors), dtype=index_type)
if self.__curindex_type == np.float64:
dists = np.empty((nqpts, num_neighbors), dtype=np.float64)
else:
dists = np.empty((nqpts, num_neighbors), dtype=np.float32)
self.__flann_parameters.update(kwargs)
flann.find_nearest_neighbors_index[
self.__curindex_type](
self.__curindex, qpts, nqpts, result, dists, num_neighbors,
pointer(self.__flann_parameters))
if num_neighbors == 1:
return (result.reshape(nqpts), dists.reshape(nqpts))
else:
return (result, dists)
''')
docstr = 'Searches for nearest neighbors using the index provided'
return_doc = zero_success
return_type = 'int'
# optional_args = ['Distance d = Distance()']
binding_argnames = [
'index_ptr',
'testset',
'tcount',
'result_ids',
'dists',
'nn',
'flann_params',
]
py_alias = 'nn_index'
py_args = ['qpts', 'num_neighbors=1', '**kwargs']
elif binding_name == 'find_nearest_neighbors':
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {{
init_flann_parameters(flann_params);
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<int> m_indices(result_ids,tcount, nn);
Matrix<DistanceType> m_dists(dists, tcount, nn);
SearchParams search_params = create_search_params(flann_params);
index->knnSearch(Matrix<ElementType>(testset, tcount, index->veclen()),
m_indices,
m_dists, nn, search_params );
return 0;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
return -1;
''')
py_source = ut.codeblock('''
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
if qpts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
if pts.dtype != qpts.dtype:
raise FLANNException('Data and query must have the same type')
pts = ensure_2d_array(pts, default_flags)
qpts = ensure_2d_array(qpts, default_flags)
npts, dim = pts.shape
nqpts = qpts.shape[0]
assert qpts.shape[1] == dim, 'data and query must have the same dims'
assert npts >= num_neighbors, 'more neighbors than there are points'
result = np.empty((nqpts, num_neighbors), dtype=index_type)
if pts.dtype == np.float64:
dists = np.empty((nqpts, num_neighbors), dtype=np.float64)
else:
dists = np.empty((nqpts, num_neighbors), dtype=np.float32)
self.__flann_parameters.update(kwargs)
flann.find_nearest_neighbors[
pts.dtype.type](
pts, npts, dim, qpts, nqpts, result, dists, num_neighbors,
pointer(self.__flann_parameters))
if num_neighbors == 1:
return (result.reshape(nqpts), dists.reshape(nqpts))
else:
return (result, dists)
''')
docstr = 'Builds an index and uses it to find nearest neighbors.'
return_doc = zero_success
py_alias = 'nn'
py_args = ['pts', 'qpts', 'num_neighbors=1', '**kwargs']
return_type = 'int'
binding_argnames = [
'dataset', 'rows', 'cols', 'testset', 'tcount', 'result_ids',
'dists', 'nn', 'flann_params'
]
optional_args = ['Distance d = Distance()']
elif binding_name == 'load_index':
c_source_part = ut.codeblock(r'''
Index<Distance>* index = new Index<Distance>(Matrix<typename Distance::ElementType>(dataset,rows,cols), SavedIndexParams(filename), d);
return index;
''')
py_source = ut.codeblock('''
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
pts = ensure_2d_array(pts, default_flags)
npts, dim = pts.shape
if self.__curindex is not None:
flann.free_index[self.__curindex_type](
self.__curindex, pointer(self.__flann_parameters))
self.__curindex = None
self.__curindex_data = None
self.__added_data = []
self.__curindex_type = None
self.__curindex = flann.load_index[pts.dtype.type](
c_char_p(to_bytes(filename)), pts, npts, dim)
if self.__curindex is None:
raise FLANNException(
('Error loading the FLANN index with filename=%r.'
' C++ may have thrown more detailed errors') % (filename,))
self.__curindex_data = pts
self.__added_data = []
self.__removed_ids = []
self.__curindex_type = pts.dtype.type
''')
docstr = 'Loads a previously saved index from a file.'
return_doc = 'index_ptr'
cpp_param_doc['dataset'] = 'The dataset corresponding to the index'
cpp_param_doc['filename'] = 'File to load the index from'
py_args = ['filename', 'pts']
return_type = 'flann_index_t'
binding_argnames = ['filename', 'dataset', 'rows', 'cols']
optional_args = ['Distance d = Distance()']
elif binding_name == 'save_index':
docstr = 'Saves the index to a file. Only the index is saved into the file, the dataset corresponding to the index is not saved.'
cpp_param_doc['index_ptr'] = 'The index that should be saved'
cpp_param_doc['filename'] = 'The filename the index should be saved to'
return_doc = 'Returns 0 on success, negative value on error'
c_source_part = ut.codeblock(r'''
Index<Distance>* index = (Index<Distance>*)index_ptr;
index->save(filename);
return 0;
''')
py_source = ut.codeblock('''
if self.__curindex is not None:
flann.save_index[self.__curindex_type](
self.__curindex, c_char_p(to_bytes(filename)))
''')
return_type = 'int'
binding_argnames = ['index_ptr', 'filename']
py_alias = None
py_args = None
elif binding_name == 'build_index':
docstr = ut.codeblock('''
Builds and returns an index. It uses autotuning if the target_precision field of index_params
is between 0 and 1, or the parameters specified if it's -1.
''')
pydoc = ut.codeblock('''
This builds and internally stores an index to be used for
future nearest neighbor matchings. It erases any previously
stored indexes, so use multiple instances of this class to
work with multiple stored indices. Use nn_index(...) to find
the nearest neighbors in this index.
pts is a 2d numpy array or matrix. All the computation is done
in np.float32 type, but pts may be any type that is convertable
to np.float32.
''')
c_source = ut.codeblock(r'''
typedef typename Distance::ElementType ElementType;
try {
init_flann_parameters(flann_params);
if (flann_params == NULL) {
throw FLANNException("The flann_params argument must be non-null");
}
IndexParams params = create_parameters(flann_params);
Index<Distance>* index = new Index<Distance>(Matrix<ElementType>(dataset,rows,cols), params, d);
index->buildIndex();
if (flann_params->algorithm==FLANN_INDEX_AUTOTUNED) {
IndexParams params = index->getParameters();
update_flann_parameters(params,flann_params);
SearchParams search_params = get_param<SearchParams>(params,"search_params");
*speedup = get_param<float>(params,"speedup");
flann_params->checks = search_params.checks;
flann_params->eps = search_params.eps;
flann_params->cb_index = get_param<float>(params,"cb_index",0.0);
}
return index;
}
catch (std::runtime_error& e) {
Logger::error("Caught exception: %s\n",e.what());
return NULL;
}
''').replace('{', '{{').replace('}', '}}')
py_source = ut.codeblock('''
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
pts = ensure_2d_array(pts, default_flags)
npts, dim = pts.shape
self.__ensureRandomSeed(kwargs)
self.__flann_parameters.update(kwargs)
if self.__curindex is not None:
flann.free_index[self.__curindex_type](
self.__curindex, pointer(self.__flann_parameters))
self.__curindex = None
speedup = c_float(0)
self.__curindex = flann.build_index[pts.dtype.type](
pts, npts, dim, byref(speedup), pointer(self.__flann_parameters))
self.__curindex_data = pts
self.__curindex_type = pts.dtype.type
params = dict(self.__flann_parameters)
params['speedup'] = speedup.value
return params
''')
# binding_argnames = ['dataset', 'rows', 'cols', 'speedup', 'flann_params']
return_doc = 'the newly created index or a number <0 for error'
cpp_param_doc[
'speedup'] = 'speedup over linear search, estimated if using autotuning, output parameter'
optional_args = ['Distance d = Distance()']
return_type = 'flann_index_t'
py_args = ['pts', '**kwargs']
binding_argnames = [
'dataset', 'rows', 'cols', 'speedup', 'flann_params'
]
elif binding_name == 'free_index':
docstr = 'Deletes an index and releases the memory used by it.'
pydoc = ut.codeblock('''
Deletes the current index freeing all the momory it uses.
The memory used by the dataset that was indexed is not freed
unless there are no other references to those numpy arrays.
''')
c_source_part = ut.codeblock(r'''
Index<Distance>* index = (Index<Distance>*)index_ptr;
delete index;
return 0;
''')
py_source = ut.codeblock('''
self.__flann_parameters.update(kwargs)
if self.__curindex is not None:
flann.free_index[self.__curindex_type](
self.__curindex, pointer(self.__flann_parameters))
self.__curindex = None
self.__curindex_data = None
self.__added_data = []
self.__removed_ids = []
''')
return_doc = zero_success
return_type = 'int'
binding_argnames = ['index_ptr', 'flann_params']
cpp_param_doc['flann_params'] = ut.textblock(
'''generic flann params (only used to specify verbosity)''')
py_alias = 'delete_index'
py_args = ['**kwargs']
elif binding_name == 'get_point':
docstr = 'Gets a point from a given index position.'
return_doc = 'pointer to datapoint or NULL on miss'
binding_argnames = ['index_ptr', 'point_id']
cpp_param_doc['point_id'] = 'index of datapoint to get.'
return_type = 'Distance::ElementType*'
elif binding_name == 'flann_get_distance_order':
docstr = ut.textblock(
'''Gets the distance order in use throughout FLANN (only applicable
if minkowski distance is in use).''')
binding_argnames = []
return_type = 'int'
else:
dictdef = {
'_template_new': {
'docstr': '',
'binding_argnames': [],
'return_type': 'int',
},
'flann_get_distance_type': {
'docstr': '',
'binding_argnames': [],
'return_type': 'int',
},
'flann_log_verbosity': {
'docstr':
ut.codeblock('''
Sets the log level used for all flann functions (unless
specified in FLANNParameters for each call
'''),
'binding_argnames': ['level'],
'return_type':
'void',
},
}
if binding_name in dictdef:
docstr = dictdef[binding_name].get('docstr', '')
binding_argnames = dictdef[binding_name]['binding_argnames']
return_type = dictdef[binding_name]['return_type']
else:
raise NotImplementedError('Unknown binding name %r' %
(binding_name, ))
if c_source is None:
if c_source_part is not None:
try_ = ut.codeblock('''
try {{
''')
throw_ = '\n' + ut.indent(
ut.codeblock('''
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
'''), ' ' * 4)
if 'index_ptr' not in binding_argnames:
throw_ = ''
if 'flann_params' in binding_argnames:
part1 = try_ + '\n' + ' init_flann_parameters(flann_params);' + throw_
else:
part1 = try_ + throw_
if return_type == 'int':
default_return = '-1'
else:
default_return = 'NULL'
part2 = ut.codeblock(r'''
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return ''' + default_return + ''';
}}
''')
c_source = part1 + '\n' + ut.indent(c_source_part,
' ' * 4) + '\n' + part2
else:
c_source = ut.codeblock('''
TODO: IMPLEMENT THIS FUNCTION WRAPPER
''')
try:
docstr_cpp = docstr[:]
if return_doc is not None:
param_docs = ut.dict_take(cpp_param_doc, binding_argnames)
cpp_param_docblock = '\n'.join([
'%s = %s' % (name, doc)
for name, doc in zip(binding_argnames, param_docs)
])
docstr_cpp += '\n\n' + 'Params:\n' + ut.indent(
cpp_param_docblock, ' ')
docstr_cpp += '\n\n' + 'Returns: ' + return_doc
if pydoc is None:
docstr_py = docstr[:]
else:
docstr_py = pydoc[:]
if py_args:
py_param_doc = cpp_param_doc.copy()
py_param_doc['pts'] = py_param_doc['dataset'].replace(
'pointer to ', '')
py_param_doc['qpts'] = (
py_param_doc['testset'].replace('pointer to ', '') +
' (may be a single point)')
py_param_doc['num_neighbors'] = py_param_doc['nn']
py_param_doc['**kwargs'] = py_param_doc['flann_params']
py_args_ = [a.split('=')[0] for a in py_args]
param_docs = ut.dict_take(py_param_doc, py_args_, '')
# py_types =
py_param_docblock = '\n'.join([
'%s: %s' % (name, doc)
for name, doc in zip(py_args_, param_docs)
])
docstr_py += '\n\n' + 'Params:\n' + ut.indent(
py_param_docblock, ' ')
except Exception as ex:
ut.printex(ex, keys=['binding_name'])
raise
pass
binding_def = {
'cpp_binding_name': cpp_binding_name,
'docstr_cpp': docstr_cpp,
'docstr_py': docstr_py,
'return_type': return_type,
'binding_argnames': binding_argnames,
'c_source': c_source,
'optional_args': optional_args,
'py_source': py_source,
'py_args': py_args,
'py_alias': py_alias,
}
return binding_def
def setup_actions_menu(mainwin, back):
""" ACTIONS MENU """
mainwin.menuActions = mainwin.menubar.newMenu('Actions')
menu = mainwin.menuActions
menu.newAction(
name='actionCompute_Occurrences',
text='Group Occurrences',
#shortcut='Ctrl+2',
triggered=back.do_group_occurrence_step)
menu.addSeparator() # ---------
menu.newAction(
name='actionDetect',
text='Run Detection',
#shortcut='Ctrl+3',
triggered=back.run_detection_step)
menu.addSeparator() # ---------
menu.newAction(name='actionQuery',
text='Query Single Annotation',
shortcut='Q',
triggered=functools.partial(back.compute_queries,
use_visual_selection=True))
menu.newAction(
name='actionBatchIntraOccurrenceQueries',
text='Query: Intra Occurrence',
triggered=functools.partial(back.compute_queries,
daids_mode=const.INTRA_OCCUR_KEY),
)
menu.newAction(
name='actionBatchVsExemplarQueries',
text='Query: vs Exemplars',
triggered=functools.partial(back.compute_queries,
daids_mode=const.VS_EXEMPLARS_KEY),
)
menu.addSeparator() # ---------
menu.newAction(name='actionSetExemplarsFromQualityAndViewpoint',
text='Set Exemplars from Quality and Viewpoint',
triggered=back.set_exemplars_from_quality_and_viewpoint_,
tooltip=ut.textblock('''
Uses the quality and viewpoint column to pick the best N exemplars
per viewpoint, per name.
'''))
menu.addSeparator() # ---------
menu.newAction(
name='actionAdvancedID',
text='Advanced ID Interface',
triggered=back.show_advanced_id_interface,
shortcut='Ctrl+G',
)
menu.newAction(name='actionRunMergeChecks',
text='Run Merge Checks (Exemplars vs Exemplars)',
triggered=back.run_merge_checks)
mainwin.mergeMenu = menu.newMenu('Other Merge Checks')
mainwin.mergeMenu.newAction(name='actionRunMergeChecks2',
text='Run Merge Checks (multitons)',
triggered=back.run_merge_checks_multitons)
menu.addSeparator() # ---------
if not const.SIMPLIFY_INTERFACE:
menu.newAction(name='actionBatchConsecutiveLocationSpeciesRename',
text='Consecutive Location+Species Rename',
triggered=back.batch_rename_consecutive_via_species_,
tooltip=ut.textblock('''
Renames ALL the names in the database to
{other_cfg.location_for_names}_{species_code}_{num}
'''))
menu.addSeparator() # ---------
menu.newAction(
name='actionShipProcessedOccurrences',
text='Ship Processed Occurrences',
tooltip='''This action will ship to WildBook any occurrences that have
been marked as processed. This can also be used to send
processed imagesets that failed to ship correctly.''',
#shortcut='Ctrl+5',
triggered=back.send_unshipped_processed_imagesets)
menu.addSeparator() # ---------
menu.newAction(text='Override All Annotation Species',
triggered=back.override_all_annotation_species)
menu.newAction(text='Rename Species',
triggered=back.update_species_nice_name)
menu.newAction(text='Delete Species',
triggered=back.delete_selected_species)
menu.addSeparator() # ---------
menu.newAction(name='actionDeleteAllImageSets',
text='Delete All ImageSets',
triggered=back.delete_all_imagesets)
menu.newAction(name='actionDelete_Image',
text='Delete Image',
triggered=back.delete_image)
menu.newAction(name='actionDelete_ANNOTATION',
text='Delete Annotation',
shortcut='Ctrl+Del',
triggered=back.delete_annot)
menu.addSeparator()
def confirm(self, event=None):
"""
CommandLine:
python -m ibeis.viz.interact.interact_query_decision --test-confirm
Example:
>>> # DISABLE_DOCTEST
>>> from ibeis.viz.interact.interact_query_decision import * # NOQA
>>> import utool as ut
>>> # build test data
>>> import ibeis
>>> ibs = ibeis.opendb('testdb1')
>>> self = ibs
>>> self.ibs = ibs
>>> selected_aids = ut.get_list_column(ibs.get_name_aids(ibs.get_valid_nids()), 0)
>>> comfirm_res = 'jeff'
>>> # execute function
>>> #result = self.confirm(event)
>>> # verify results
>>> #print(result)
"""
print('[interact_query_decision] Confirming selected animals.')
selected_aids = [
aid for aid in self.comp_aids
if aid is not None and self.aid_checkbox_states[aid]
]
if len(selected_aids) == 0:
print('[interact_query_decision] Confirming no match.')
chosen_aids = []
if self.other_checkbox_states['none']:
chosen_aids = 'newname'
elif self.other_checkbox_states['junk']:
chosen_aids = 'junk'
else:
msg = 'INTERACT_QUERY_DECISION IMPOSSIBLE STATE'
raise AssertionError(msg)
elif len(selected_aids) == 1:
print('[interact_query_decision] Confirming single match')
chosen_aids = selected_aids
else:
print('[interact_query_decision] Confirming merge')
msg = ut.textblock('''
You have selected more than one animal as a match to the query
animal. By doing this you are telling IBEIS that these are ALL
the SAME ANIMAL. \n\n\nIf this is not what you want, click
Cancel. If it is what you want, choose one of the names below
as the name to keep.
''')
selected_names = self.ibs.get_annot_names(selected_aids)
options = selected_names
parent = None
title = 'Confirm Merge'
merge_name = guitool.user_option(parent,
msg=msg,
title=title,
options=options)
if merge_name is None:
print('[interact_query_decision] cancelled merge')
self.update_callback()
self.backend_callback()
self.show_page()
return
else:
print('[interact_query_decision] confirmed merge')
is_merge_name = [
merge_name == name_ for name_ in selected_names
]
chosen_aids = ut.sortedby(selected_aids, is_merge_name)[::-1]
print('[interact_query_decision] Calling update callbacks')
self.update_callback()
self.backend_callback()
print('[interact_query_decision] Calling decision callback')
print('[interact_query_decision] self.name_decision_callback = %r' %
(self.name_decision_callback, ))
if isinstance(chosen_aids, six.string_types):
# hack for string non-match commands
chosen_names = chosen_aids
else:
chosen_names = self.ibs.get_annot_names(chosen_aids)
self.name_decision_callback(chosen_names)
print(
'[interact_query_decision] sent name_decision_callback(chosen_names=%r)'
% (chosen_names, ))
def define_flann_bindings(binding_name):
"""
Define the binding names for flann
"""
# default c source
c_source = None
optional_args = None
c_source_part = None
py_source = None
py_alias = None
py_args = None
pydoc = None
cpp_param_doc = {
'cols': 'number of columns in the dataset (feature dimensionality)',
'dataset': 'pointer to a data set stored in row major order',
'dists': ut.packtext(
'''pointer to matrix for the distances of the nearest neighbors of
the testset features in the dataset'''),
'flann_params': 'generic flann parameters',
'index_ptr': 'the index (constructed previously using flann_build_index)',
'nn': 'how many nearest neighbors to return',
'rebuild_threshold': ut.packtext(
'''reallocs index when it grows by factor of `rebuild_threshold`.
A smaller value results is more space efficient but less
computationally efficient. Must be greater than 1.'''),
'result_ids': ut.packtext(
'''pointer to matrix for the indices of the nearest neighbors of
the testset features in the dataset (must have tcount number of
rows and nn number of columns)'''),
'rows': 'number of rows (features) in the dataset',
'tcount': ut.packtext(
'''number of rows (features) in the query dataset (same
dimensionality as features in the dataset)'''),
'testset': 'pointer to a query set stored in row major order',
'level': 'verbosity level'
}
standard_csource = ut.codeblock(
r'''
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
return index->{cpp_binding_name}();
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
throw;
}}
'''
)
return_doc = None
cpp_binding_name = binding_name
zero_success = 'zero or a number <0 for error'
if binding_name == 'clean_removed_points':
cpp_binding_name = ut.to_camel_case(binding_name)
return_type = 'void'
docstr = 'Deletes removed points in index?'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'veclen':
return_type = 'int'
docstr = 'Returns number of features in this index'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'size':
return_type = 'int'
docstr = 'returns The dimensionality of the features in this index.'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'getType':
return_type = 'flann_algorithm_t'
docstr = 'returns The index type (kdtree, kmeans,...)'
binding_argnames = ['index_ptr']
c_source = standard_csource
elif binding_name == 'used_memory':
docstr = ut.codeblock(
'''
Returns the amount of memory (in bytes) used by the index
index_ptr = pointer to pre-built index.
Returns: int
'''
)
c_source = ut.codeblock(
r'''
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
return index->usedMemory();
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
'''
)
py_source = ut.codeblock(
'''
if self.__curindex is None:
return 0
return flann.used_memory[self.__curindex_type](self.__curindex)
''')
binding_argnames = ['index_ptr']
return_type = 'int'
elif binding_name == 'add_points':
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<ElementType> points = Matrix<ElementType>(points, rows, index->veclen());
index->addPoints(points, rebuild_threshold);
return 0;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
'''
)
py_source = ut.codeblock(
'''
if new_pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % new_pts.dtype)
if new_pts.dtype != self.__curindex_type:
raise FLANNException('New points must have the same type')
new_pts = ensure_2d_array(new_pts, default_flags)
rows = new_pts.shape[0]
flann.add_points[self.__curindex_type](self.__curindex, new_pts, rows, rebuild_threshold)
return self.__added_data.append(new_pts)
''')
#return_type = 'void'
return_type = 'int'
docstr = 'Adds points to pre-built index.'
if False:
binding_argnames = [
'index_ptr',
'points',
'rows',
'cols', # TODO: can remove
'rebuild_threshold',
]
else:
binding_argnames = [
'index_ptr',
'points',
'rows',
'rebuild_threshold',
]
return_doc = '0 if success otherwise -1'
py_args = ['new_pts', 'rebuild_threshold=2.']
cpp_param_doc['points'] = 'pointer to array of points'
elif binding_name == 'remove_point':
c_source = ut.codeblock(
r'''
size_t point_id(point_id_uint);
try {{
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
index->removePoint(point_id);
return 0;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
'''
)
py_source = ut.codeblock(
'''
flann.remove_point[self.__curindex_type](self.__curindex, point_id)
self.__removed_ids.append(point_id)
''')
#return_type = 'void'
return_type = 'int'
docstr = 'Removes a point from the index'
return_doc = zero_success
cpp_param_doc['point_id'] = 'point id to be removed'
cpp_param_doc['index_ptr'] = 'The index that should be modified'
binding_argnames = ['index_ptr', 'point_id']
elif binding_name == 'remove_points':
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
try {{
if (index_ptr==NULL) {{
thow FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
index->removePoints(id_list, num);
return;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return;
}}
'''
)
py_source = ut.codeblock(
'''
id_list = np.array(id_list, dtype=np.int32)
num = len(id_list)
flann.remove_points[self.__curindex_type](self.__curindex, id_list, num)
self.__removed_ids.extend(id_list)
''')
cpp_param_doc['index_ptr'] = 'The index that should be modified'
cpp_param_doc['id_list'] = 'list of point ids to be removed'
cpp_param_doc['num'] = 'number of points in id_list'
docstr = 'Removes multiple points from the index'
return_doc = 'void'
py_args = ['id_list']
return_type = 'void'
binding_argnames = ['index_ptr', 'id_list', 'num']
elif binding_name == 'compute_cluster_centers':
docstr = ut.textblock(
r'''
Clusters the features in the dataset using a hierarchical kmeans
clustering approach. This is significantly faster than using a
flat kmeans clustering for a large number of clusters.
''')
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {
init_flann_parameters(flann_params);
Matrix<ElementType> inputData(dataset,rows,cols);
KMeansIndexParams params(flann_params->branching, flann_params->iterations, flann_params->centers_init, flann_params->cb_index);
Matrix<DistanceType> centers(result_centers, clusters,cols);
int clusterNum = hierarchicalClustering<Distance>(inputData, centers, params, d);
return clusterNum;
}
catch (std::runtime_error& e) {
Logger::error("Caught exception: %s\n",e.what());
return -1;
}
'''.replace('{', '{{').replace('}', '}}')
)
py_source = ut.codeblock(
'''
# First verify the paremeters are sensible.
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
if int(branch_size) != branch_size or branch_size < 2:
raise FLANNException('branch_size must be an integer >= 2.')
branch_size = int(branch_size)
if int(num_branches) != num_branches or num_branches < 1:
raise FLANNException('num_branches must be an integer >= 1.')
num_branches = int(num_branches)
if max_iterations is None:
max_iterations = -1
else:
max_iterations = int(max_iterations)
# init the arrays and starting values
pts = ensure_2d_array(pts, default_flags)
npts, dim = pts.shape
num_clusters = (branch_size - 1) * num_branches + 1
if pts.dtype.type == np.float64:
result = np.empty((num_clusters, dim), dtype=np.float64)
else:
result = np.empty((num_clusters, dim), dtype=np.float32)
# set all the parameters appropriately
self.__ensureRandomSeed(kwargs)
params = {'iterations': max_iterations,
'algorithm': 'kmeans',
'branching': branch_size,
'random_seed': kwargs['random_seed']}
self.__flann_parameters.update(params)
numclusters = flann.compute_cluster_centers[pts.dtype.type](
pts, npts, dim, num_clusters, result,
pointer(self.__flann_parameters))
if numclusters <= 0:
raise FLANNException('Error occured during clustering procedure.')
if dtype is None:
return result
else:
return dtype(result)
''').replace('}', '}}').replace('{', '{{')
return_doc = ut.packtext(
'''number of clusters computed or a number <0 for error. This
number can be different than the number of clusters requested, due
to the way hierarchical clusters are computed. The number of
clusters returned will be the highest number of the form
(branch_size-1)*K+1 smaller than the number of clusters
requested.''')
cpp_param_doc['clusters'] = 'number of cluster to compute'
cpp_param_doc['result_centers'] = 'memory buffer where the output cluster centers are stored'
cpp_param_doc['flann_params'] = 'generic flann parameters and index_params used to specify the kmeans tree parameters (branching factor, max number of iterations to use)'
return_type = 'int'
binding_argnames = ['dataset', 'rows', 'cols', 'clusters', 'result_centers', 'flann_params']
optional_args = ['Distance d = Distance()']
py_alias = 'hierarchical_kmeans'
py_args = 'pts, branch_size, num_branches, max_iterations=None, dtype=None, **kwargs'.split(', ')
elif binding_name == 'radius_search':
docstr = ut.codeblock(
r'''
Performs an radius search using an already constructed index.
In case of radius search, instead of always returning a predetermined
number of nearest neighbours (for example the 10 nearest neighbours), the
search will return all the neighbours found within a search radius
of the query point.
The check parameter in the FLANNParameters below sets the level of approximation
for the search by only visiting "checks" number of features in the index
(the same way as for the KNN search). A lower value for checks will give
a higher search speedup at the cost of potentially not returning all the
neighbours in the specified radius.
''')
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {{
init_flann_parameters(flann_params);
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<int> m_result_ids(result_ids, 1, max_nn);
Matrix<DistanceType> m_dists(dists1d, 1, max_nn);
SearchParams search_params = create_search_params(flann_params);
int count = index->radiusSearch(Matrix<ElementType>(query1d, 1, index->veclen()),
m_result_ids,
m_dists, radius, search_params );
return count;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
''')
py_source = ut.codeblock(
'''
if self.__curindex is None:
raise FLANNException(
'build_index(...) method not called first or current index deleted.')
if query.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % query.dtype)
if self.__curindex_type != query.dtype.type:
raise FLANNException('Index and query must have the same type')
npts, dim = self.get_indexed_shape()
assert(query.shape[0] == dim), 'data and query must have the same dims'
result = np.empty(npts, dtype=index_type)
if self.__curindex_type == np.float64:
dists = np.empty(npts, dtype=np.float64)
else:
dists = np.empty(npts, dtype=np.float32)
self.__flann_parameters.update(kwargs)
nn = flann.radius_search[
self.__curindex_type](
self.__curindex, query, result, dists, npts, radius,
pointer(self.__flann_parameters))
return (result[0:nn], dists[0:nn])
''')
cpp_param_doc['index_ptr'] = 'the index'
cpp_param_doc['query1d'] = 'query point'
cpp_param_doc['dists1d'] = 'similar, but for storing distances'
cpp_param_doc['result_ids'] = 'array for storing the indices found (will be modified)'
cpp_param_doc['max_nn'] = 'size of arrays result_ids and dists1d'
cpp_param_doc['radius'] = 'search radius (squared radius for euclidian metric)'
return_doc = 'number of neighbors found or <0 for an error'
return_type = 'int'
binding_argnames = ['index_ptr', 'query1d', 'result_ids', 'dists1d', 'max_nn',
'radius', 'flann_params', ]
py_alias = 'nn_radius'
py_args = 'query, radius, **kwargs'.split(', ')
elif binding_name == 'find_nearest_neighbors_index':
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {
init_flann_parameters(flann_params);
if (index_ptr==NULL) {
throw FLANNException("Invalid index");
}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<int> m_indices(result_ids,tcount, nn);
Matrix<DistanceType> m_dists(dists, tcount, nn);
SearchParams search_params = create_search_params(flann_params);
index->knnSearch(Matrix<ElementType>(testset, tcount, index->veclen()),
m_indices,
m_dists, nn, search_params );
return 0;
}
catch (std::runtime_error& e) {
Logger::error("Caught exception: %s\n",e.what());
return -1;
}
return -1;
'''
).replace('{', '{{').replace('}', '}}')
py_source = ut.codeblock(
'''
if self.__curindex is None:
raise FLANNException(
'build_index(...) method not called first or current index deleted.')
if qpts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % qpts.dtype)
if self.__curindex_type != qpts.dtype.type:
raise FLANNException('Index and query must have the same type')
qpts = ensure_2d_array(qpts, default_flags)
npts, dim = self.get_indexed_shape()
if qpts.size == dim:
qpts.reshape(1, dim)
nqpts = qpts.shape[0]
assert qpts.shape[1] == dim, 'data and query must have the same dims'
assert npts >= num_neighbors, 'more neighbors than there are points'
result = np.empty((nqpts, num_neighbors), dtype=index_type)
if self.__curindex_type == np.float64:
dists = np.empty((nqpts, num_neighbors), dtype=np.float64)
else:
dists = np.empty((nqpts, num_neighbors), dtype=np.float32)
self.__flann_parameters.update(kwargs)
flann.find_nearest_neighbors_index[
self.__curindex_type](
self.__curindex, qpts, nqpts, result, dists, num_neighbors,
pointer(self.__flann_parameters))
if num_neighbors == 1:
return (result.reshape(nqpts), dists.reshape(nqpts))
else:
return (result, dists)
'''
)
docstr = 'Searches for nearest neighbors using the index provided'
return_doc = zero_success
return_type = 'int'
# optional_args = ['Distance d = Distance()']
binding_argnames = ['index_ptr', 'testset', 'tcount', 'result_ids',
'dists', 'nn', 'flann_params', ]
py_alias = 'nn_index'
py_args = ['qpts', 'num_neighbors=1', '**kwargs']
elif binding_name == 'find_nearest_neighbors':
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
typedef typename Distance::ResultType DistanceType;
try {{
init_flann_parameters(flann_params);
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
Index<Distance>* index = (Index<Distance>*)index_ptr;
Matrix<int> m_indices(result_ids,tcount, nn);
Matrix<DistanceType> m_dists(dists, tcount, nn);
SearchParams search_params = create_search_params(flann_params);
index->knnSearch(Matrix<ElementType>(testset, tcount, index->veclen()),
m_indices,
m_dists, nn, search_params );
return 0;
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return -1;
}}
return -1;
'''
)
py_source = ut.codeblock(
'''
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
if qpts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
if pts.dtype != qpts.dtype:
raise FLANNException('Data and query must have the same type')
pts = ensure_2d_array(pts, default_flags)
qpts = ensure_2d_array(qpts, default_flags)
npts, dim = pts.shape
nqpts = qpts.shape[0]
assert qpts.shape[1] == dim, 'data and query must have the same dims'
assert npts >= num_neighbors, 'more neighbors than there are points'
result = np.empty((nqpts, num_neighbors), dtype=index_type)
if pts.dtype == np.float64:
dists = np.empty((nqpts, num_neighbors), dtype=np.float64)
else:
dists = np.empty((nqpts, num_neighbors), dtype=np.float32)
self.__flann_parameters.update(kwargs)
flann.find_nearest_neighbors[
pts.dtype.type](
pts, npts, dim, qpts, nqpts, result, dists, num_neighbors,
pointer(self.__flann_parameters))
if num_neighbors == 1:
return (result.reshape(nqpts), dists.reshape(nqpts))
else:
return (result, dists)
''')
docstr = 'Builds an index and uses it to find nearest neighbors.'
return_doc = zero_success
py_alias = 'nn'
py_args = ['pts', 'qpts', 'num_neighbors=1', '**kwargs']
return_type = 'int'
binding_argnames = ['dataset', 'rows', 'cols', 'testset', 'tcount',
'result_ids', 'dists', 'nn', 'flann_params']
optional_args = ['Distance d = Distance()']
elif binding_name == 'load_index':
c_source_part = ut.codeblock(
r'''
Index<Distance>* index = new Index<Distance>(Matrix<typename Distance::ElementType>(dataset,rows,cols), SavedIndexParams(filename), d);
return index;
'''
)
py_source = ut.codeblock(
'''
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
pts = ensure_2d_array(pts, default_flags)
npts, dim = pts.shape
if self.__curindex is not None:
flann.free_index[self.__curindex_type](
self.__curindex, pointer(self.__flann_parameters))
self.__curindex = None
self.__curindex_data = None
self.__added_data = []
self.__curindex_type = None
self.__curindex = flann.load_index[pts.dtype.type](
c_char_p(to_bytes(filename)), pts, npts, dim)
if self.__curindex is None:
raise FLANNException(
('Error loading the FLANN index with filename=%r.'
' C++ may have thrown more detailed errors') % (filename,))
self.__curindex_data = pts
self.__added_data = []
self.__removed_ids = []
self.__curindex_type = pts.dtype.type
''')
docstr = 'Loads a previously saved index from a file.'
return_doc = 'index_ptr'
cpp_param_doc['dataset'] = 'The dataset corresponding to the index'
cpp_param_doc['filename'] = 'File to load the index from'
py_args = ['filename', 'pts']
return_type = 'flann_index_t'
binding_argnames = ['filename', 'dataset', 'rows', 'cols']
optional_args = ['Distance d = Distance()']
elif binding_name == 'save_index':
docstr = 'Saves the index to a file. Only the index is saved into the file, the dataset corresponding to the index is not saved.'
cpp_param_doc['index_ptr'] = 'The index that should be saved'
cpp_param_doc['filename'] = 'The filename the index should be saved to'
return_doc = 'Returns 0 on success, negative value on error'
c_source_part = ut.codeblock(
r'''
Index<Distance>* index = (Index<Distance>*)index_ptr;
index->save(filename);
return 0;
''')
py_source = ut.codeblock(
'''
if self.__curindex is not None:
flann.save_index[self.__curindex_type](
self.__curindex, c_char_p(to_bytes(filename)))
''')
return_type = 'int'
binding_argnames = ['index_ptr', 'filename']
py_alias = None
py_args = None
elif binding_name == 'build_index':
docstr = ut.codeblock(
'''
Builds and returns an index. It uses autotuning if the target_precision field of index_params
is between 0 and 1, or the parameters specified if it's -1.
''')
pydoc = ut.codeblock(
'''
This builds and internally stores an index to be used for
future nearest neighbor matchings. It erases any previously
stored indexes, so use multiple instances of this class to
work with multiple stored indices. Use nn_index(...) to find
the nearest neighbors in this index.
pts is a 2d numpy array or matrix. All the computation is done
in np.float32 type, but pts may be any type that is convertable
to np.float32.
''')
c_source = ut.codeblock(
r'''
typedef typename Distance::ElementType ElementType;
try {
init_flann_parameters(flann_params);
if (flann_params == NULL) {
throw FLANNException("The flann_params argument must be non-null");
}
IndexParams params = create_parameters(flann_params);
Index<Distance>* index = new Index<Distance>(Matrix<ElementType>(dataset,rows,cols), params, d);
index->buildIndex();
if (flann_params->algorithm==FLANN_INDEX_AUTOTUNED) {
IndexParams params = index->getParameters();
update_flann_parameters(params,flann_params);
SearchParams search_params = get_param<SearchParams>(params,"search_params");
*speedup = get_param<float>(params,"speedup");
flann_params->checks = search_params.checks;
flann_params->eps = search_params.eps;
flann_params->cb_index = get_param<float>(params,"cb_index",0.0);
}
return index;
}
catch (std::runtime_error& e) {
Logger::error("Caught exception: %s\n",e.what());
return NULL;
}
''').replace('{', '{{').replace('}', '}}')
py_source = ut.codeblock(
'''
if pts.dtype.type not in allowed_types:
raise FLANNException('Cannot handle type: %s' % pts.dtype)
pts = ensure_2d_array(pts, default_flags)
npts, dim = pts.shape
self.__ensureRandomSeed(kwargs)
self.__flann_parameters.update(kwargs)
if self.__curindex is not None:
flann.free_index[self.__curindex_type](
self.__curindex, pointer(self.__flann_parameters))
self.__curindex = None
speedup = c_float(0)
self.__curindex = flann.build_index[pts.dtype.type](
pts, npts, dim, byref(speedup), pointer(self.__flann_parameters))
self.__curindex_data = pts
self.__curindex_type = pts.dtype.type
params = dict(self.__flann_parameters)
params['speedup'] = speedup.value
return params
''')
# binding_argnames = ['dataset', 'rows', 'cols', 'speedup', 'flann_params']
return_doc = 'the newly created index or a number <0 for error'
cpp_param_doc['speedup'] = 'speedup over linear search, estimated if using autotuning, output parameter'
optional_args = ['Distance d = Distance()']
return_type = 'flann_index_t'
py_args = ['pts', '**kwargs']
binding_argnames = ['dataset', 'rows', 'cols', 'speedup', 'flann_params']
elif binding_name == 'free_index':
docstr = 'Deletes an index and releases the memory used by it.'
pydoc = ut.codeblock(
'''
Deletes the current index freeing all the momory it uses.
The memory used by the dataset that was indexed is not freed
unless there are no other references to those numpy arrays.
''')
c_source_part = ut.codeblock(
r'''
Index<Distance>* index = (Index<Distance>*)index_ptr;
delete index;
return 0;
''')
py_source = ut.codeblock(
'''
self.__flann_parameters.update(kwargs)
if self.__curindex is not None:
flann.free_index[self.__curindex_type](
self.__curindex, pointer(self.__flann_parameters))
self.__curindex = None
self.__curindex_data = None
self.__added_data = []
self.__removed_ids = []
''')
return_doc = zero_success
return_type = 'int'
binding_argnames = ['index_ptr', 'flann_params']
cpp_param_doc['flann_params'] = ut.textblock(
'''generic flann params (only used to specify verbosity)''')
py_alias = 'delete_index'
py_args = ['**kwargs']
elif binding_name == 'get_point':
docstr = 'Gets a point from a given index position.'
return_doc = 'pointer to datapoint or NULL on miss'
binding_argnames = ['index_ptr', 'point_id']
cpp_param_doc['point_id'] = 'index of datapoint to get.'
return_type = 'Distance::ElementType*'
elif binding_name == 'flann_get_distance_order':
docstr = ut.textblock(
'''Gets the distance order in use throughout FLANN (only applicable
if minkowski distance is in use).''')
binding_argnames = []
return_type = 'int'
else:
dictdef = {
'_template_new': {
'docstr': '',
'binding_argnames': [],
'return_type': 'int',
},
'flann_get_distance_type': {
'docstr': '',
'binding_argnames': [],
'return_type': 'int',
},
'flann_log_verbosity': {
'docstr': ut.codeblock(
'''
Sets the log level used for all flann functions (unless
specified in FLANNParameters for each call
'''
),
'binding_argnames': ['level'],
'return_type': 'void',
},
}
if binding_name in dictdef:
docstr = dictdef[binding_name].get('docstr', '')
binding_argnames = dictdef[binding_name]['binding_argnames']
return_type = dictdef[binding_name]['return_type']
else:
raise NotImplementedError('Unknown binding name %r' % (binding_name,))
if c_source is None:
if c_source_part is not None:
try_ = ut.codeblock(
'''
try {{
'''
)
throw_ = '\n' + ut.indent(ut.codeblock(
'''
if (index_ptr==NULL) {{
throw FLANNException("Invalid index");
}}
'''
), ' ' * 4)
if 'index_ptr' not in binding_argnames:
throw_ = ''
if 'flann_params' in binding_argnames:
part1 = try_ + '\n' + ' init_flann_parameters(flann_params);' + throw_
else:
part1 = try_ + throw_
if return_type == 'int':
default_return = '-1'
else:
default_return = 'NULL'
part2 = ut.codeblock(
r'''
}}
catch (std::runtime_error& e) {{
Logger::error("Caught exception: %s\n",e.what());
return ''' + default_return + ''';
}}
'''
)
c_source = part1 + '\n' + ut.indent(c_source_part, ' ' * 4) + '\n' + part2
else:
c_source = ut.codeblock(
'''
TODO: IMPLEMENT THIS FUNCTION WRAPPER
'''
)
try:
docstr_cpp = docstr[:]
if return_doc is not None:
param_docs = ut.dict_take(cpp_param_doc, binding_argnames)
cpp_param_docblock = '\n'.join(
['%s = %s' % (name, doc)
for name, doc in zip(binding_argnames, param_docs)])
docstr_cpp += '\n\n' + 'Params:\n' + ut.indent(cpp_param_docblock, ' ')
docstr_cpp += '\n\n' + 'Returns: ' + return_doc
if pydoc is None:
docstr_py = docstr[:]
else:
docstr_py = pydoc[:]
if py_args:
py_param_doc = cpp_param_doc.copy()
py_param_doc['pts'] = py_param_doc['dataset'].replace('pointer to ', '')
py_param_doc['qpts'] = (py_param_doc['testset'].replace(
'pointer to ', '') + ' (may be a single point)')
py_param_doc['num_neighbors'] = py_param_doc['nn']
py_param_doc['**kwargs'] = py_param_doc['flann_params']
py_args_ = [a.split('=')[0] for a in py_args]
param_docs = ut.dict_take(py_param_doc, py_args_, '')
# py_types =
py_param_docblock = '\n'.join(['%s: %s' % (name, doc)
for name, doc in zip(py_args_, param_docs)])
docstr_py += '\n\n' + 'Params:\n' + ut.indent(py_param_docblock, ' ')
except Exception as ex:
ut.printex(ex, keys=['binding_name'])
raise
pass
binding_def = {
'cpp_binding_name': cpp_binding_name,
'docstr_cpp': docstr_cpp,
'docstr_py': docstr_py,
'return_type': return_type,
'binding_argnames': binding_argnames,
'c_source': c_source,
'optional_args': optional_args,
'py_source': py_source,
'py_args': py_args,
'py_alias': py_alias,
}
return binding_def
def confirm(self, event=None):
"""
CommandLine:
python -m ibeis.viz.interact.interact_query_decision --test-confirm
Example:
>>> # DISABLE_DOCTEST
>>> from ibeis.viz.interact.interact_query_decision import * # NOQA
>>> import utool as ut
>>> # build test data
>>> import ibeis
>>> ibs = ibeis.opendb('testdb1')
>>> self = ibs
>>> self.ibs = ibs
>>> selected_aids = ut.get_list_column(ibs.get_name_aids(ibs.get_valid_nids()), 0)
>>> comfirm_res = 'jeff'
>>> # execute function
>>> #result = self.confirm(event)
>>> # verify results
>>> #print(result)
"""
print('[interact_query_decision] Confirming selected animals.')
selected_aids = [aid for aid in self.comp_aids
if aid is not None and self.aid_checkbox_states[aid]]
if len(selected_aids) == 0:
print('[interact_query_decision] Confirming no match.')
chosen_aids = []
if self.other_checkbox_states['none']:
chosen_aids = 'newname'
elif self.other_checkbox_states['junk']:
chosen_aids = 'junk'
else:
msg = 'INTERACT_QUERY_DECISION IMPOSSIBLE STATE'
raise AssertionError(msg)
elif len(selected_aids) == 1:
print('[interact_query_decision] Confirming single match')
chosen_aids = selected_aids
else:
print('[interact_query_decision] Confirming merge')
msg = ut.textblock(
'''
You have selected more than one animal as a match to the query
animal. By doing this you are telling IBEIS that these are ALL
the SAME ANIMAL. \n\n\nIf this is not what you want, click
Cancel. If it is what you want, choose one of the names below
as the name to keep.
''')
selected_names = self.ibs.get_annot_names(selected_aids)
options = selected_names
parent = None
title = 'Confirm Merge'
merge_name = guitool.user_option(parent, msg=msg, title=title,
options=options)
if merge_name is None:
print('[interact_query_decision] cancelled merge')
self.update_callback()
self.backend_callback()
self.show_page()
return
else:
print('[interact_query_decision] confirmed merge')
is_merge_name = [merge_name == name_ for name_ in selected_names]
chosen_aids = ut.sortedby(selected_aids, is_merge_name)[::-1]
print('[interact_query_decision] Calling update callbacks')
self.update_callback()
self.backend_callback()
print('[interact_query_decision] Calling decision callback')
print('[interact_query_decision] self.name_decision_callback = %r' % (self.name_decision_callback,))
if isinstance(chosen_aids, six.string_types):
# hack for string non-match commands
chosen_names = chosen_aids
else:
chosen_names = self.ibs.get_annot_names(chosen_aids)
self.name_decision_callback(chosen_names)
print('[interact_query_decision] sent name_decision_callback(chosen_names=%r)' % (chosen_names,))
def setup_actions_menu(mainwin, back):
""" ACTIONS MENU """
mainwin.menuActions = guitool.newMenu(mainwin, mainwin.menubar, 'menuActions', 'Actions')
menu = mainwin.menuActions
menu.newAction(
name='actionCompute_Encounters',
text='Group Encounters',
#shortcut='Ctrl+2',
slot_fn=back.compute_encounters)
menu.addSeparator() # ---------
menu.newAction(
name='actionDetect',
text='Run Detection',
#shortcut='Ctrl+3',
slot_fn=back.run_detection)
menu.addSeparator() # ---------
menu.newAction(
name='actionQuery',
text='Query Single Annotation',
shortcut='Q',
slot_fn=functools.partial(back.compute_queries, use_visual_selection=True))
menu.newAction(
name='actionBatchIntraEncounterQueries',
text='Query: Intra Encounter',
slot_fn=functools.partial(back.compute_queries, daids_mode=const.INTRA_ENC_KEY),
)
menu.newAction(
name='actionBatchVsExemplarQueries',
text='Query: vs Exemplars',
slot_fn=functools.partial(back.compute_queries, daids_mode=const.VS_EXEMPLARS_KEY),
)
menu.addSeparator() # ---------
menu.newAction(
name='actionSetExemplarsFromQualityAndViewpoint',
text='Set Exemplars from Quality and Viewpoint',
slot_fn=back.set_exemplars_from_quality_and_viewpoint,
tooltip=ut.textblock(
'''
Uses the quality and viewpoint column to pick the best N exemplars
per viewpoint, per name.
''')
)
menu.addSeparator() # ---------
menu.newAction(
name='actionRunMergeChecks',
text='Run Merge Checks (Exemplars vs Exemplars)',
slot_fn=back.run_merge_checks)
menu.addSeparator() # ---------
if not const.SIMPLIFY_INTERFACE:
menu.newAction(
name='actionBatchConsecutiveLocationSpeciesRename',
text='Consecutive Location+Species Rename',
slot_fn=back.batch_rename_consecutive_via_species,
tooltip=ut.textblock(
'''
Renames ALL the names in the database to
{other_cfg.location_for_names}_{species_code}_{num}
''')
)
menu.addSeparator() # ---------
menu.newAction(
name='actionShipProcessedEncounters',
text='Ship Processed Encounters',
tooltip='''This action will ship to WildBook any encounters that have
been marked as processed. This can also be used to send
processed encounters that failed to ship correctly.''',
#shortcut='Ctrl+5',
slot_fn=back.send_unshipped_processed_encounters)
menu.addSeparator() # ---------
menu.newAction(
text='Override All Annotation Species',
slot_fn=back.override_all_annotation_species)
menu.newAction(
text='Rename Species',
slot_fn=back.update_species_nice_name)
menu.newAction(
text='Delete Species',
slot_fn=back.delete_selected_species)
menu.addSeparator() # ---------
menu.newAction(
name='actionDeleteAllEncounters',
text='Delete All Encounters',
slot_fn=back.delete_all_encounters)
menu.newAction(
name='actionDelete_Image',
text='Delete Image',
slot_fn=back.delete_image)
menu.newAction(
name='actionDelete_ANNOTATION',
text='Delete Annotation',
shortcut='Ctrl+Del',
slot_fn=back.delete_annot)
menu.addSeparator()
