def _construct_mnn(t1_cells, t2_cells, data_df, n_neighbors,device,n_jobs=-2):
# FUnction to construct mutually nearest neighbors bewteen two points
if device == "gpu":
from cuml import NearestNeighbors
nbrs = NearestNeighbors(n_neighbors=n_neighbors,
metric='euclidean')
elif device == "cpu":
from sklearn.neighbors import NearestNeighbors
nbrs = NearestNeighbors(n_neighbors=n_neighbors,
metric='euclidean', n_jobs=n_jobs)
print(f't+1 neighbors of t...')
nbrs.fit(data_df.loc[t1_cells, :].values)
t1_nbrs = nbrs.kneighbors_graph(
data_df.loc[t2_cells, :].values, mode='distance')
print(f't neighbors of t+1...')
nbrs.fit(data_df.loc[t2_cells, :].values)
t2_nbrs = nbrs.kneighbors_graph(
data_df.loc[t1_cells, :].values, mode='distance')
# Mututally nearest neighbors
mnn = t2_nbrs.multiply(t1_nbrs.T)
mnn = mnn.sqrt()
return mnn
def find_matching_image_with_rapids():
model = EfficientNetB0(weights='imagenet',
include_top=False,
pooling='avg',
input_shape=None)
train_gen = DataGenerator(train, batch_size=128)
image_embeddings = model.predict(train_gen, verbose=1)
print('image embeddings shape is', image_embeddings.shape)
# After fitting KNN, we will display some example rows of train and their 8 closest other images in train (based EffNetB0 image embeddings).
KNN = 50
model = NearestNeighbors(n_neighbors=KNN)
model.fit(image_embeddings)
distances, indices = model.kneighbors(image_embeddings)
for k in range(180, 190):
plt.figure(figsize=(20, 3))
plt.plot(np.arange(50), cupy.asnumpy(distances[k, ]), 'o-')
plt.title('Image Distance From Train Row %i to Other Train Rows' % k,
size=16)
plt.ylabel('Distance to Train Row %i' % k, size=14)
plt.xlabel('Index Sorted by Distance to Train Row %i' % k, size=14)
plt.show()
cluster = train.loc[cupy.asnumpy(indices[k, :8])]
displayDF(cluster, random=False, ROWS=2, COLS=4)
def find_similar_image():
KNN = 50
if len(test) == 3:
KNN = 2
model = NearestNeighbors(n_neighbors=KNN)
model.fit(image_embeddings)
preds = []
CHUNK = 1024 * 4
print('Finding similar images...')
CTS = len(image_embeddings) // CHUNK
if len(image_embeddings) % CHUNK != 0:
CTS += 1
for j in range(CTS):
a = j * CHUNK
b = (j + 1) * CHUNK
b = min(b, len(image_embeddings))
print('chunk', a, 'to', b)
distances, indices = model.kneighbors(image_embeddings[a:b, ])
for k in range(b - a):
IDX = np.where(distances[k,] < 6.0)[0]
IDS = indices[k, IDX]
o = test.iloc[IDS].posting_id.values
preds.append(o)
del model, distances, indices, image_embeddings, embeds
_ = gc.collect()
test['preds2'] = preds
test.head()
def get_image_predictions(df, embeddings, threshold=0.0):
if len(df) > 3:
KNN = 50
else:
KNN = 3
model = NearestNeighbors(n_neighbors=KNN, metric='cosine')
model.fit(embeddings)
distances, indices = model.kneighbors(embeddings)
predictions = []
for k in tqdm(range(embeddings.shape[0])):
idx = np.where(distances[k, ] < threshold)[0]
ids = indices[k, idx]
posting_ids = df['posting_id'].iloc[ids].values
if len(posting_ids) >= 2:
idx_s = np.where(distances[k, ] < threshold - 0.08888)[0]
ids_s = indices[k, idx_s]
posting_ids_b = df['posting_id'].iloc[ids_s].values
if len(posting_ids_b) >= 2:
predictions.append(posting_ids_b)
else:
predictions.append(posting_ids)
else:
idx = np.where(distances[k, ] < 0.51313)[0]
ids = indices[k, idx]
posting_ids = df['posting_id'].iloc[ids].values
predictions.append(posting_ids[:2])
del model, distances, indices
gc.collect()
return predictions
def get_preds(embs_path, threshold):
image_embeddings = np.load(embs_path)['embeddings']
KNN = 50
if len(df) == 3:
KNN = 2
model = NearestNeighbors(n_neighbors=KNN)
model.fit(image_embeddings)
image_embeddings = cupy.array(image_embeddings)
preds = []
CHUNK = 1024 * 4
# print('Finding similar images...')
CTS = len(image_embeddings) // CHUNK
if len(image_embeddings) % CHUNK != 0:
CTS += 1
for j in range(CTS):
a = j * CHUNK
b = (j + 1) * CHUNK
b = min(b, len(image_embeddings))
cts = cupy.matmul(image_embeddings, image_embeddings[a:b].T).T
for k in range(b - a):
IDX = cupy.where(cts[k, ] > threshold)[0]
IDX = cupy.asnumpy(IDX)
o = cpu_df.iloc[IDX].posting_id.values
preds.append(o)
return preds
def compute_neighbors_rapids(X: np.ndarray,
n_neighbors: int,
metric: _Metric = 'euclidean'):
"""Compute nearest neighbors using RAPIDS cuml.
Parameters
----------
X: array of shape (n_samples, n_features)
The data to compute nearest neighbors for.
n_neighbors
The number of neighbors to use.
metric
The metric to use to compute distances in high dimensional space.
This string must match a valid predefined metric in RAPIDS cuml.
Returns
-------
**knn_indices**, **knn_dists** : np.arrays of shape (n_observations, n_neighbors)
"""
from cuml.neighbors import NearestNeighbors
nn = NearestNeighbors(n_neighbors=n_neighbors, metric=metric)
X_contiguous = np.ascontiguousarray(X, dtype=np.float32)
nn.fit(X_contiguous)
knn_dist, knn_indices = nn.kneighbors(X_contiguous)
return knn_indices, knn_dist
def _find_distance_threshold(
self,
features,
posting_ids: np.ndarray,
thresholds: List[float],
) -> Tuple[float, float, List[List[str]]]:
features = F.normalize(torch.from_numpy(features)).numpy()
with TimeUtil.timer("nearest neighbor search"):
model = NearestNeighbors(n_neighbors=len(self.valid_df), n_jobs=32)
model.fit(features)
distances, indices = model.kneighbors(features)
FileUtil.save_npy(
distances,
self.config.dir_config.output_dir
/ f"distances_{self.fold}_{self.current_epoch:02d}.npy",
)
FileUtil.save_npy(
indices,
self.config.dir_config.output_dir
/ f"indices_{self.fold}_{self.current_epoch:02d}.npy",
)
best_score = 0
best_threshold = -1
best_y_pred: List[List[str]] = []
for threshold in thresholds:
y_pred = []
for i in range(len(distances)):
IDX = np.where(distances[i] < threshold)[0]
if len(IDX) < self.config.inference_config.min_indices:
IDX = list(range(self.config.inference_config.min_indices))
idxs = indices[i, IDX]
y_pred.append(posting_ids[idxs])
scores = MetricUtil.f1_scores(self.valid_df["target"].tolist(), y_pred)
precisions, recalls = MetricUtil.precision_recall(
self.valid_df["target"].tolist(), y_pred
)
self.valid_df["score"] = scores
self.valid_df["precision"] = precisions
self.valid_df["recall"] = recalls
selected_score = self.valid_df["score"].mean()
_p_mean = self.valid_df["precision"].mean()
_r_mean = self.valid_df["recall"].mean()
print(
f"----------- valid f1: {selected_score} precision: {_p_mean} recall: {_r_mean} threshold: {threshold} ------------"
)
if selected_score > best_score:
best_score = selected_score
best_threshold = threshold
best_y_pred = y_pred
return best_score, best_threshold, best_y_pred
def get_image_neighbors(df, embeddings, threshold=args.threshold):
n_neighbors = args.n_neighbors_max if len(df) > 3 else args.n_neighbors_min
model_nearest_neighbors = NearestNeighbors(n_neighbors=n_neighbors)
model_nearest_neighbors.fit(embeddings)
distances, indices = model_nearest_neighbors.kneighbors(embeddings)
predictions = []
for k in range(embeddings.shape[0]):
idx = np.where(distances[k] < threshold)[0]
ids = indices[k, idx]
posting_ids = df['posting_id'].iloc[ids].values
predictions.append(posting_ids)
del model_nearest_neighbors, distances, indices
gc.collect()
return predictions
def test_fuzzy_simplicial_set(n_rows, n_features, n_neighbors,
precomputed_nearest_neighbors):
n_clusters = 30
random_state = 42
metric = 'euclidean'
X, _ = make_blobs(n_samples=n_rows,
centers=n_clusters,
n_features=n_features,
random_state=random_state)
if precomputed_nearest_neighbors:
nn = NearestNeighbors(n_neighbors=n_neighbors, metric=metric)
nn.fit(X)
knn_dists, knn_indices = nn.kneighbors(X,
n_neighbors,
return_distance=True)
cu_fss_graph = cu_fuzzy_simplicial_set(X,
n_neighbors,
random_state,
metric,
knn_indices=knn_indices,
knn_dists=knn_dists)
knn_indices = knn_indices.get()
knn_dists = knn_dists.get()
ref_fss_graph = ref_fuzzy_simplicial_set(
X,
n_neighbors,
random_state,
metric,
knn_indices=knn_indices,
knn_dists=knn_dists)[0].tocoo()
else:
cu_fss_graph = cu_fuzzy_simplicial_set(X, n_neighbors, random_state,
metric)
X = X.get()
ref_fss_graph = ref_fuzzy_simplicial_set(X, n_neighbors, random_state,
metric)[0].tocoo()
cu_fss_graph = cu_fss_graph.todense()
ref_fss_graph = cp.sparse.coo_matrix(ref_fss_graph).todense()
assert correctness_sparse(ref_fss_graph,
cu_fss_graph,
atol=0.1,
rtol=0.2,
threshold=0.95)
def get_image_neighbors(df, embeddings, KNN=50):
model = NearestNeighbors(n_neighbors=KNN)
model.fit(embeddings)
distances, indices = model.kneighbors(embeddings)
threshold = 4.5
predictions = []
for k in tqdm(range(embeddings.shape[0])):
idx = np.where(distances[k, ] < threshold)[0]
ids = indices[k, idx]
posting_ids = df['posting_id'].iloc[ids].values
predictions.append(posting_ids)
del model, distances, indices
gc.collect()
return df, predictions
def reduce_dimensionality(self, embeddings):
"""Reduce dimensionality of embeddings using UMAP and train a UMAP model
Args:
embeddings (cupy.ndarray): The extracted embeddings using the
sentence transformer module.
Returns:
umap_embeddings: The reduced embeddings
"""
m_cos = NearestNeighbors(n_neighbors=15, metric="cosine")
m_cos.fit(embeddings)
knn_graph_cos = m_cos.kneighbors_graph(embeddings, mode="distance")
u1 = UMAP(n_neighbors=15, n_components=5, min_dist=0.0)
umap_embeddings = u1.fit_transform(embeddings, knn_graph=knn_graph_cos)
return umap_embeddings
def get_image_neighbors(df, embeddings, KNN=50):
model = NearestNeighbors(n_neighbors=KNN) # 创建knn模型
model.fit(embeddings) # 训练features
distances, indices = model.kneighbors(embeddings) # 获得图片之间的距离（相似度）
predictions = []
for k in tqdm(range(embeddings.shape[0])): # 每张图片都拿出来两两比对
idx = np.where(
distances[k, ] < CFG.img_thres)[0] # 设置一个thres（阈值），来确定匹配的严格程度
# 对于没有匹配到的其他图片的图片，我们放宽阈值再匹配一次
if len(idx) == 1:
idx = np.where(distances[k, ] < (CFG.img_thres + CFG.addition))[0]
ids = indices[k, idx]
posting_ids = df['posting_id'].iloc[ids].values # 输出匹配的图片
predictions.append(posting_ids)
del model, distances, indices
gc.collect()
return predictions
def compute_neighbors_rapids(X: np.ndarray, n_neighbors: int):
"""Compute nearest neighbors using RAPIDS cuml.
Parameters
----------
X: array of shape (n_samples, n_features)
The data to compute nearest neighbors for.
n_neighbors
The number of neighbors to use.
Returns
-------
**knn_indices**, **knn_dists** : np.arrays of shape (n_observations, n_neighbors)
"""
from cuml.neighbors import NearestNeighbors
nn = NearestNeighbors(n_neighbors=n_neighbors)
X_contiguous = np.ascontiguousarray(X, dtype=np.float32)
nn.fit(X_contiguous)
knn_distsq, knn_indices = nn.kneighbors(X_contiguous)
return knn_indices, np.sqrt(
knn_distsq) # cuml uses sqeuclidean metric so take sqrt
def find_similar_titles_with_rapids_knn():
"""
First we will extract text embeddings using RAPIDS cuML's TfidfVectorizer.
This will turn every title into a one-hot-encoding of the words present.
We will then compare one-hot-encodings with RAPIDS cuML KNN to find title's that are similar.
:return:
"""
# LOAD TRAIN UNTO THE GPU WITH CUDF
train_gf = cudf.read_csv('../input/shopee-product-matching/train.csv')
print('train shape is', train_gf.shape)
train_gf.head()
# Extract Text Embeddings with RAPIDS TfidfVectorizer¶
# TfidfVectorizer returns a cupy sparse matrix.
# Afterward we convert to a cupy dense matrix and feed that into RAPIDS cuML KNN.
model = TfidfVectorizer(stop_words='english', binary=True)
text_embeddings = model.fit_transform(train_gf.title).toarray()
print('text embeddings shape is', text_embeddings.shape)
# After fitting KNN, we will display some example rows of train and their 10 closest other titles in train (based on word count one-hot-encoding).
KNN = 50
model = NearestNeighbors(n_neighbors=KNN)
model.fit(text_embeddings)
distances, indices = model.kneighbors(text_embeddings)
for k in range(5):
plt.figure(figsize=(20, 3))
plt.plot(np.arange(50), cupy.asnumpy(distances[k, ]), 'o-')
plt.title('Text Distance From Train Row %i to Other Train Rows' % k,
size=16)
plt.ylabel('Distance to Train Row %i' % k, size=14)
plt.xlabel('Index Sorted by Distance to Train Row %i' % k, size=14)
plt.show()
print(train_gf.loc[cupy.asnumpy(indices[k, :10]),
['title', 'label_group']])
def setNodeData(self, nodes_data: xa.DataArray, **kwargs):
print(
f"{self.__class__.__name__}[{hex(id(self))}].setNodeData: input shape = {nodes_data.shape}"
)
if self.reset or (self.nodes is None):
if (nodes_data.size > 0):
t0 = time.time()
self.nodes = cudf.DataFrame({
icol: nodes_data[:, icol]
for icol in range(nodes_data.shape[1])
})
self.nnd = NearestNeighbors(n_neighbors=self.nneighbors)
self.nnd.fit(self.nodes)
self.D, self.I = self.nnd.kneighbors(self.nodes,
return_distance=True)
dt = (time.time() - t0)
print(
f"Computed NN Graph with {self.nnd.n_neighbors} neighbors and {nodes_data.shape[0]} verts in {dt} sec ({dt/60} min)"
)
print(
f" ---> Indices shape = {self.I.shape}, Distances shape = {self.D.shape} "
)
else:
print("No data available for this block")
def compute_neighbors_sklearn(X: np.ndarray, n_neighbors: int):
"""Compute nearest neighbors using sklearn
Parameters
----------
X: array of shape (n_samples, n_features)
The data to compute nearest neighbors for.
n_neighbors
The number of neighbors to use.
Returns
-------
**knn_indices**, **knn_dists** : np.arrays of shape (n_observations, n_neighbors)
"""
from sklearn.neighbors import NearestNeighbors
import time
t0 = time.time()
nn = NearestNeighbors(n_neighbors=n_neighbors)
X_contiguous = np.ascontiguousarray(X, dtype=np.float32)
nn.fit(X_contiguous)
knn_dist, knn_indices = nn.kneighbors(X_contiguous)
print("Here", time.time() - t0)
return knn_indices, knn_dist
def KNN_predict(df, embeddings, KNN=50, thresh=None, thresh_range=None):
'''
thresh_range: np.arrange for threshold selection
thresh: distance threshold for result matching
image: 2.7, tfidf: 0.6
image: list(np.arange(2,10,0.5))
text : list(np.arange(0.1, 1, 0.1))
'''
assert ((thresh is None) or (thresh_range is None)), "Must provide either `thresh` or `thresh_range`"
if thresh_range is not None:
assert 'matches' in df.columns, "Cannot perform threshold selection on testing data"
model = NearestNeighbors(n_neighbors = KNN)
model.fit(embeddings)
distances, indices = model.kneighbors(embeddings)
# Iterate through different thresholds to maximize cv, run this in interactive mode, then replace else clause with a solid threshold
thresholds_scores = None
if thresh is None:
thresholds = thresh_range
scores = []
recalls = []
precisions = []
for threshold in thresholds:
predictions = []
for k in range(embeddings.shape[0]):
idx = np.where(distances[k,] < threshold)[0]
ids = indices[k,idx]
posting_ids = ' '.join(df['posting_id'].iloc[ids].values)
predictions.append(posting_ids)
df['pred_matches'] = predictions
f1, precision, recall = f1_score(df['matches'], df['pred_matches'])
print(f'Threshold {threshold:.2f}: F1 {f1.mean():.4f} Precision {precision.mean():.4f} Recall {recall.mean():.4f}')
scores.append(f1.mean())
recalls.append(recall.mean())
precisions.append(precision.mean())
thresholds_scores = pd.DataFrame({
'thresholds': thresholds,
'scores': scores,
'recalls': recalls,
'precisions': precisions
})
max_score = thresholds_scores[thresholds_scores['scores'] == thresholds_scores['scores'].max()]
best_threshold = max_score['thresholds'].values[0]
best_score = max_score['scores'].values[0]
print(f'Our best score is {best_score} and has a threshold {best_threshold}')
thresh = best_threshold
# Because we are predicting the test set that have 70K images and different label groups, confidence should be smaller
predictions = []
for k in tqdm(range(embeddings.shape[0])):
idx = np.where(distances[k,] < thresh)[0]
ids = indices[k,idx]
posting_ids = df['posting_id'].iloc[ids].values
predictions.append(posting_ids)
del model, distances, indices
gc.collect()
return df, predictions, thresholds_scores
imagefeat.append(feat)
# In[11]:
from sklearn.preprocessing import normalize
# l2 norm to kill all the sim in 0-1
imagefeat = np.vstack(imagefeat)
imagefeat = normalize(imagefeat)
# In[12]:
KNN = 50
if len(test) == 3: KNN = 2
model = NearestNeighbors(n_neighbors=KNN)
model.fit(imagefeat)
# In[13]:
preds = []
CHUNK = 1024 * 4
imagefeat = cupy.array(imagefeat)
print('Finding similar images...')
CTS = len(imagefeat) // CHUNK
if len(imagefeat) % CHUNK != 0: CTS += 1
for j in range(CTS):
a = j * CHUNK
def augmented_affinity_matrix(
data_df,
timepoints,
timepoint_connections,
n_neighbors=30,
n_jobs=-2,
pc_components=1000,
device="cpu",
):
"""Function for max min sampling of waypoints
:param data_df: Normalized data frame. Data frame should be sorted according to the timepoints
:param timepoints: Panadas series indicating timepoints for each cell in data_df
:param timepoint_connections: Links between timepoints
:param n_neighbors: Number of nearest neighbors for graph construction
:param n_jobs: Nearest Neighbors will be computed in parallel using n_jobs.
:param pc_components: Minimum number of principal components to use. Specify `None` to use pre-computed components
:return: Affinity matrix augmented to mutually nearest neighbors
"""
# Timepoints nad data_df should in same order
timepoints = timepoints[data_df.index]
cell_order = data_df.index
# Time point cells and indices
tp_cells = pd.Series()
tp_offset = pd.Series()
offset = 0
for i in timepoints.unique():
tp_offset[i] = offset
tp_cells[i] = list(timepoints.index[timepoints == i])
offset += len(tp_cells[i])
# Run PCA to denoise the dropouts
if pc_components is None:
pca_projections = data_df
else:
pca_projections, _ = utils.run_pca(data_df,device, n_components=pc_components)
# Nearest neighbor graph construction and affinity matrix
print('Nearest neighbor computation...')
# --------------------------------------------------------------------------
# nbrs = NearestNeighbors(n_neighbors=n_neighbors,
# metric='euclidean', n_jobs=-2)
# nbrs.fit(pca_projections.values)
# dists, _ = nbrs.kneighbors(pca_projections.values)
# adj = nbrs.kneighbors_graph(pca_projections.values, mode='distance')
# # Scaling factors for affinity matrix construction
# ka = np.int(n_neighbors / 3)
# scaling_factors = pd.Series(dists[:, ka], index=cell_order)
# # Affinity matrix
# nn_aff = _convert_to_affinity(adj, scaling_factors, True)
# --------------------------------------------------------------------------
if device == "cpu":
temp = sc.AnnData(data_df.values)
sc.pp.neighbors(temp, n_pcs=0, n_neighbors=n_neighbors)
# maintaining backwards compatibility to Scanpy `sc.pp.neighbors`
try:
kNN = temp.uns['neighbors']['distances']
except KeyError:
kNN = temp.obsp['distances']
elif device == "gpu":
from cuml.neighbors import NearestNeighbors
nn = NearestNeighbors(n_neighbors=n_neighbors,metric="euclidean")
X_contiguous = np.ascontiguousarray(data_df.values)
nn.fit(X_contiguous)
kNN = nn.kneighbors_graph(X_contiguous,mode="distance")
kNN.setdiag(0)
kNN.eliminate_zeros()
# Adaptive k
adaptive_k = int(np.floor(n_neighbors / 3))
scaling_factors = np.zeros(data_df.shape[0])
for i in np.arange(len(scaling_factors)):
scaling_factors[i] = np.sort(kNN.data[kNN.indptr[i]:kNN.indptr[i + 1]])[adaptive_k - 1]
scaling_factors = pd.Series(scaling_factors, index=cell_order)
# Affinity matrix
nn_aff = _convert_to_affinity(kNN, scaling_factors, device, True)
# Mututally nearest neighbor affinity matrix
# Initilze mnn affinity matrix
N = len(cell_order)
full_mnn_aff = csr_matrix(([0], ([0], [0])), [N, N])
for i in timepoint_connections.index:
t1, t2 = timepoint_connections.loc[i, :].values
print(f'Constucting affinities between {t1} and {t2}...')
# MNN matrix and distance to ka the distance
t1_cells = tp_cells[t1]
t2_cells = tp_cells[t2]
mnn = _construct_mnn(t1_cells, t2_cells, pca_projections,
n_neighbors, device, n_jobs)
# MNN Scaling factors
# Distance to the adaptive neighbor
ka_dists = pd.Series(0.0, index=t1_cells + t2_cells)
# T1 scaling factors
ka_dists[t1_cells] = _mnn_ka_distances(mnn, n_neighbors)
# T2 scaling factors
ka_dists[t2_cells] = _mnn_ka_distances(mnn.T, n_neighbors)
# Scaling factors
mnn_scaling_factors = pd.Series(0.0, index=cell_order)
mnn_scaling_factors[t1_cells] = _mnn_scaling_factors(
ka_dists[t1_cells], scaling_factors, device)
mnn_scaling_factors[t2_cells] = _mnn_scaling_factors(
ka_dists[t2_cells], scaling_factors, device)
# MNN affinity matrix
full_mnn_aff = full_mnn_aff + \
_mnn_affinity(mnn, mnn_scaling_factors,
tp_offset[t1], tp_offset[t2], device)
# Symmetrize the affinity matrix and return
aff = nn_aff + nn_aff.T + full_mnn_aff + full_mnn_aff.T
return aff, nn_aff + nn_aff.T
def computeGrid(img_collection, X_2d, out_res, out_dim):
#grid = np.zeros(())
out = np.ones((out_dim * out_res, out_dim * out_res, 4), dtype=np.uint8)
nn = NearestNeighbors(n_neighbors=1)
d = {}
# TODO: assumes unique
#for i, xy in enumerate(X_2d):
# d[tuple(xy)] = i
def build(remaining):
xs = sorted(remaining, key=lambda x: x[0])
ys = sorted(remaining, key=lambda x: x[1])
X = np.zeros((out_dim * out_dim, 2), np.float32)
for x in range(out_dim):
for y in range(out_dim):
X[y * out_dim + x] = np.array([
xs[int(x * len(xs) / out_dim)][0],
ys[int(y * len(ys) / out_dim)][1]
])
#X = np.array(X)
#print(X.shape)
nn.fit(remaining)
X_cudf = cudf.DataFrame(X)
distances, indices = nn.kneighbors(X_cudf)
return indices
#remaining = X_2d
indices = build(X_2d)
seen = {}
#for i, x in enumerate(xs):
#for j, y in enumerate(ys):
for x in range(out_dim):
for y in range(out_dim):
done = False
e = 0
while not done:
#X = (xs[int(x * len(xs) / out_dim)], ys[int(y * len(ys) / out_dim)])
#X_cudf = cudf.DataFrame(X)
#distances, indices = nn.kneighbors(X_cudf)
p = nearest = indices[(y * out_dim + x + e) % len(indices)]
if p in seen:
e += 1
#print("rebuild")
#remaining = [X_2d[x] for i, x in enumerate(X_2d) if not i in seen]
#indices = build(remaining)
else:
seen[p] = True
done = True
#print("nearest", nearest)
#p = d[tuple(nearest)]
#grid[i][j] = img_collection[p]
pos = (x, y)
print("xyp", x, y, p)
img = img_collection[p]
h_range = x * out_res
w_range = y * out_res
#print("range", h_range, h_range + out_res, w_range, w_range + out_res)
out[h_range:h_range + out_res,
w_range:w_range + out_res, :] = readImage(img, out_res)
#break
#break
#im = image.array_to_img(out)
im = Image.fromarray(out)
im.save(out_dir + out_name, quality=100)
def spreadXY(X_2d, threshold, speed):
'spreads items until distance is greater than threshold'
import cudf
from cuml.neighbors import NearestNeighbors
def kernel(x, y, outx, outy, threshold2):
for i, (x2, y2) in enumerate(zip(x, y)):
d = math.sqrt(x2 * x2 + y2 * y2)
if 0 < d <= threshold2:
outx[i] = x2 / d
outy[i] = y2 / d
else:
outx[i] = 0
outy[i] = 0
print('spreadXY')
length = len(X_2d)
X = cudf.DataFrame()
X['x'] = X_2d[0:length, 0]
X['y'] = X_2d[0:length, 1]
k = 8
scale = 10000
threshold *= scale
speed *= scale
X = X.mul(scale)
#X = np.copy(X_2d[:length])
for i in range(20):
nn = NearestNeighbors(n_neighbors=k)
nn.fit(X)
distances, indices = nn.kneighbors(X)
#print(distances.shape)
joins = []
s = X.sum()
print("iteration", i, "sum dist", s)
newX = X
for j in range(k):
join = indices.drop([x for x in range(k) if x != j
]) #.rename(mapper={j: 'x'}, columns=[j])
join = join.merge(X, how='left', left_on=[j], right_index=True)
join = join.drop(j)
v = join.sub(X)
v = v.apply_rows(kernel,
incols=['x', 'y'],
outcols=dict(outx=np.float32, outy=np.float32),
kwargs=dict(threshold2=threshold))
v = v.drop(['x', 'y'])
v = v.rename(columns={'outx': 'x', 'outy': 'y'})
newX = newX.sub(v.mul(speed))
#newX = newX.add(1)
#v = v.query('x * x + y * y <= ' + str(threshold * threshold))
#print("newX")
#print(newX)
X = newX
s = X.sum()
print("iteration", i, "sum dist", s)
X = X.truediv(scale)
X = np.array(X.as_matrix())
print(X.shape)
return X
def mk_nnmdl(feats, n_nbrs=N_NBRS):
nnmdl = NearestNeighbors(N_NBRS, metric="cosine")
nnmdl.fit(feats)
return nnmdl
def diffusion(
adata: AnnData,
n_components=10,
knn=30,
alpha=0,
multiscale: bool = True,
n_eigs: int = None,
device="cpu",
n_pcs=50,
copy=False,
):
"""\
Wrapper to generate diffusion maps using Palantir.
Parameters
----------
adata
Annotated data matrix.
use_highly_variable
Use only variable genes for calculating PC components.
n_components
Number of diffusion components.
knn
Number of nearest neighbors for graph construction.
alpha
Normalization parameter for the diffusion operator.
multiscale
Whether to get mutliscale diffusion space
(calls palantir.utils.determine_multiscale_space).
n_eigs
if multiscale is True, how much components to retain.
device
Run method on either `cpu` or on `gpu`.
do_PCA
Whether to perform PCA or not.
n_pcs
Number of PC components.
seed
Get reproducible results for the GPU implementation.
copy
Return a copy instead of writing to adata.
Returns
-------
adata : anndata.AnnData
if `copy=True` it returns AnnData, else it update field to `adata`:
`.obsm['X_diffusion']`
if `multiscale = False`, diffusion space.
`.obsm['X_multiscale_diffusion']`
if `multiscale = True`, multiscale diffusion space.
`.uns['diffusion']`
dict containing results from Palantir.
"""
logg.info("Running Diffusion maps ", reset=True)
data_df = pd.DataFrame(adata.obsm["X_pca"], index=adata.obs_names)
if device == "cpu":
from palantir.utils import run_diffusion_maps
res = run_diffusion_maps(data_df,
n_components=n_components,
knn=knn,
alpha=alpha)
# code converted in GPU, not reproducible!
elif device == "gpu":
logg.warn(
"GPU implementation uses eigsh from cupy.sparse, which is not currently reproducible and can give unstable results!"
)
import cupy as cp
from cupyx.scipy.sparse import csr_matrix as csr_matrix_gpu
from cupyx.scipy.sparse.linalg import eigsh
# Determine the kernel
N = data_df.shape[0]
if not issparse(data_df):
from cuml.neighbors import NearestNeighbors
nn = NearestNeighbors(n_neighbors=knn, metric="euclidean")
X_contiguous = np.ascontiguousarray(data_df.values)
nn.fit(X_contiguous)
kNN = nn.kneighbors_graph(X_contiguous, mode="distance")
kNN.setdiag(0)
kNN.eliminate_zeros()
# Adaptive k
adaptive_k = int(np.floor(knn / 3))
adaptive_std = np.zeros(N)
for i in np.arange(len(adaptive_std)):
adaptive_std[i] = np.sort(
kNN.data[kNN.indptr[i]:kNN.indptr[i + 1]])[adaptive_k - 1]
# Kernel
x, y, dists = find(kNN)
# X, y specific stds
dists = dists / adaptive_std[x]
W = csr_matrix((np.exp(-dists), (x, y)), shape=[N, N])
# Diffusion components
kernel = W + W.T
else:
kernel = data_df
# Markov
D = np.ravel(kernel.sum(axis=1))
if alpha > 0:
# L_alpha
D[D != 0] = D[D != 0]**(-alpha)
mat = csr_matrix((D, (range(N), range(N))), shape=[N, N])
kernel = mat.dot(kernel).dot(mat)
D = np.ravel(kernel.sum(axis=1))
D[D != 0] = 1 / D[D != 0]
kernel = csr_matrix_gpu(kernel)
D = csr_matrix_gpu((cp.array(D), (cp.arange(N), cp.arange(N))),
shape=(N, N))
T = D.dot(kernel)
# Eigen value dcomposition
D, V = eigsh(T, n_components, tol=1e-4, maxiter=1000)
D, V = D.get(), V.get()
inds = np.argsort(D)[::-1]
D = D[inds]
V = V[:, inds]
# Normalize
for i in range(V.shape[1]):
V[:, i] = V[:, i] / np.linalg.norm(V[:, i])
# Create are results dictionary
res = {"T": T.get(), "EigenVectors": V, "EigenValues": D}
res["EigenVectors"] = pd.DataFrame(res["EigenVectors"])
if not issparse(data_df):
res["EigenVectors"].index = data_df.index
res["EigenValues"] = pd.Series(res["EigenValues"])
res["kernel"] = kernel.get()
if multiscale:
logg.info(" determining multiscale diffusion space")
from palantir.utils import determine_multiscale_space
adata.obsm["X_diffusion_multiscale"] = determine_multiscale_space(
res, n_eigs=n_eigs).values
logstr = " .obsm['X_diffusion_multiscale'], multiscale diffusion space.\n"
else:
adata.obsm["X_diffusion"] = res["EigenVectors"].iloc[:, 1:].values
logstr = " .obsm['X_diffusion'], diffusion space.\n"
adata.uns["diffusion"] = res
logg.info(" finished",
time=True,
end=" " if settings.verbosity > 2 else "\n")
logg.hint("added \n" + logstr +
" .uns['diffusion'] dict containing diffusion maps results.")
