Coverage for pyhiperta/waveform_indexing.py: 100%

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1"""Implements the indexing/mapping of waveforms from 1D array (hexagonal structure) to 2D square array. 

2 

3The 1D array representation is suited for vectorization of "per-element" operations such as calibration, 

4Hillas computation, etc. while the 2D square representation is faster for operations requiring neighbors 

5look-up, such as the tail-cut cleaning. It is faster to copy the data from one representation to the other 

6than to perform the cleaning with the 1D representation. 

7""" 

8 

9from typing import Tuple 

10 

11import numpy as np 

12from scipy.spatial import cKDTree 

13 

14 

15def _get_neighbors_indices(pixel_positions: np.ndarray) -> np.ndarray: 

16 """Get the indices of the pixel neighbors in the array, for each pixel. 

17 

18 Parameters 

19 ---------- 

20 pixel_positions : np.ndarray 

21 Positions of the pixels in the camera. 1st dimension is the "x" axis, 2nd dimension is "y". 

22 Shape: (2, number_of_pixels) 

23 

24 Notes 

25 ----- 

26 The returned array has shape (Number_of_pixels, 6) even though some pixels have less than 6 neighbors. When that 

27 is the case, the "extra-neighbors" have indices greater or equal than the number of pixels (invalid indices!) 

28 

29 Warnings 

30 -------- 

31 This function is only intended to work for hexagonal camera pixel positions. It assumes a pixel has at most 

32 6 neighbors and the neigbors are placed on a hexagonal grid. 

33 

34 Returns 

35 ------- 

36 np.ndarray 

37 Indices of the pixels neighbors, per pixel. Shape: (Number_of_pixels, 6) 

38 """ 

39 

40 dist_kdtree = cKDTree(pixel_positions.transpose()) 

41 

42 # Query the tree for the 1st neighbours of each pixel to get the distance between 1st neighbours 

43 # We query the tree for neighbour 2, because we query the tree for points identical to the tree points, 

44 # so the first neighbour will have distance 0 and be the pixels themselves. 

45 pixel_distances, _ = dist_kdtree.query(dist_kdtree.data, k=list(range(2, 3)), p=2, workers=-1) 

46 dist_1st_neighbour = pixel_distances.min() 

47 

48 # Now query the tree for all neighbours at most (1 + sqrt(3)) / 2 to get all 1st neighbours 

49 # We query for 6 neighbours, but not all pixels have 6 neighbours. When that is the case the 

50 # neighbours indices of the are set to a value > the number of pixels. 

51 _, neighbors_indices = dist_kdtree.query( 

52 pixel_positions.transpose(), 

53 k=list(range(2, 8)), # get 2nd to 7th neighbours 

54 distance_upper_bound=(1.0 + np.sqrt(3)) / 2.0 * dist_1st_neighbour, 

55 p=2, # 2 norm 

56 workers=-1, # use all cpus 

57 ) 

58 return neighbors_indices 

59 

60 

61def waveform_1D_to_2D_maps(pixel_positions: np.ndarray) -> Tuple[np.ndarray, np.ndarray]: 

62 """Create the 2D waveform array with "squared geometry" and 1D to 2D indices maps. 

63 

64 To perform fast "neighbour looking" operations such as convolution we need to store the waveform 

65 as a 2D array. To fit the hexagonal geometry of the camera into a 2D square grid (the 2D array) 

66 we perform a rotation (to align an axis with the 2D array axis) and then deform the other axis to 

67 align the hexagonal neighbour on the square grid. 

68 If we represent the pixels by their index in the 1D array: 

69 0 1 1 4 

70 2 3 4 -> 0 3 6 

71 5 6 2 5 

72 The algorithm is: 

73 - find 3 neighbours forming a triangle in the hexagonal representation. 

74 The pixels should be such that: the left-most pixel is in between the other 

75 two pixels on the y coordinate, eg: 

76 x 

77 x 

78 x 

79 Such a combination is always possible as the angle in the triangles is 60° and 

80 we search a space of 90°. The goal of this is to use the left-most pixel as our 

81 2D grid origin, and the other pixels coordinates will give us the rotation and 

82 deformation. 

83 In the example, the chosen are pixels are 0, 1 and 3. (1's y is equal or higher than 0's y) 

84 - Rotate all pixels coordinates such that the "down" neighbour is aligned with the 2D 

85 grid rows 

86 x x 

87 x -> 

88 x x x 

89 - Normalize the distances between pixels, so that a pixel is at distance 1 from another 

90 on row and column axis (makes next step easier). 

91 - "Deform" along the row axis to align the pixels on the 2D columns. This is a linear 

92 transformation of the x coordinate with respect to the y coordinate: 

93 ___x x ___ is the deformation to apply for a distance of +1 y 

94 -> 

95 x x x x 

96 - Bin the pixel positions to get their index in the 2D array. This gives the 1D to 2D 

97 indices maps. 

98 

99 Notes 

100 ----- 

101 This function is slow and runs only on cpu (scipy.cKDTree). It should be used only once to 

102 get the mappings for a given camera geometry. 

103 

104 Parameters 

105 ---------- 

106 pixel_positions : np.array 

107 2D array (shape: (2, N_pixels)) containing the pixels x and y coordinates. This should 

108 be the actual pixels positions in the camera. It is important that the referential in 

109 which the position are measured has equal metrics on both axis (1m in the real world 

110 is 1 on x _and_ y axis) 

111 

112 Returns 

113 ------- 

114 Tuple[np.ndarray, np.ndarray] 

115 Row and column indices (shape (N_pixels,) each) to use as 1D to 2D indexing maps. 

116 """ 

117 

118 neighbors_indices = _get_neighbors_indices(pixel_positions) 

119 

120 # find three points that are: 

121 # - all neighbours of each other 

122 # - the 1 point is the left most point (minimal x) 

123 # - the 2nd point is the higher point (max y) 

124 # - the 3rd point is the lower (min y) 

125 def find_neighbours_trio(): 

126 # Try all pixel as the left-most pixel 

127 for idx_left_most_p, left_most_p_neighbours in enumerate(neighbors_indices): 

128 # for all neighbours to left-most pixel 

129 for idx_up_neighbour in left_most_p_neighbours: 

130 if ( 

131 idx_up_neighbour < pixel_positions.shape[1] # valid neighbour 

132 and pixel_positions[0, idx_left_most_p] <= pixel_positions[0, idx_up_neighbour] 

133 and pixel_positions[1, idx_left_most_p] <= pixel_positions[1, idx_up_neighbour] 

134 ): # We have a good higher point. Now search for a most down point. 

135 for idx_down_neighbour in neighbors_indices[idx_up_neighbour]: 

136 if ( 

137 idx_down_neighbour < pixel_positions.shape[1] # valid neighbour 

138 and idx_down_neighbour in left_most_p_neighbours # also a neighbour of left-most 

139 and pixel_positions[0, idx_left_most_p] <= pixel_positions[0, idx_down_neighbour] 

140 and pixel_positions[1, idx_left_most_p] >= pixel_positions[1, idx_down_neighbour] 

141 ): 

142 return (idx_left_most_p, idx_up_neighbour, idx_down_neighbour) 

143 raise ValueError("Could not find trio of points matching conditions.") 

144 

145 idx_left_most, idx_up_neighbour, idx_down_neighbour = find_neighbours_trio() 

146 

147 # Get the angle required to align the left-most - down-most points line to the x axis 

148 # That is the angle between the points line and the x-axis (not the reverse ! orientation is important) 

149 # 

150 # x left-most - x down-most 

151 # .___________________________ 

152 # | 

153 # | y left-most - y down-most 

154 # | 

155 # . 

156 psi = np.arctan2( 

157 pixel_positions[1, idx_left_most] - pixel_positions[1, idx_down_neighbour], 

158 pixel_positions[0, idx_down_neighbour] - pixel_positions[0, idx_left_most], 

159 ) 

160 # Apply rotation 

161 pixel_positions = np.array([[np.cos(psi), -np.sin(psi)], [np.sin(psi), np.cos(psi)]]) @ pixel_positions 

162 

163 # Normalize the neighbours distance for both axis (make neighbours distance 1 on x and y) 

164 pixel_positions[0, :] *= 1.0 / (pixel_positions[0, idx_down_neighbour] - pixel_positions[0, idx_left_most]) 

165 pixel_positions[1, :] *= 1.0 / (pixel_positions[1, idx_up_neighbour] - pixel_positions[1, idx_left_most]) 

166 # Apply linear deformation to the x coordinate based on y coordinate 

167 pixel_positions[0, :] -= (pixel_positions[1, :] - pixel_positions[1, idx_left_most]) * ( 

168 pixel_positions[0, idx_up_neighbour] - pixel_positions[0, idx_left_most] 

169 ) 

170 

171 # Bin the pixel coordinates to find their index in 2D array 

172 # After the normalization and deformation the pixels are placed at integer values on the grid 

173 # To make sure the points are not near the bins edge, make the bins shifted by 0.5 

174 # The values are then floored and converted to int by the astype 

175 # Note: - what binning x would do: (x - (min(x) - shift)) / bin_size (with integer division) 

176 # - bin size is 1.0, so no need to divide. 

177 # - row indices are reversed, because the position in the matrix start in the top left, not 

178 # bottom left as the y coordinates do. 

179 row_indices = (pixel_positions[1] - (pixel_positions[1].min() - 0.5)).astype(np.int32) 

180 row_indices = row_indices.max() - row_indices 

181 col_indices = (pixel_positions[0] - (pixel_positions[0].min() - 0.5)).astype(np.int32) 

182 

183 return (row_indices, col_indices) 

184 

185 

186def waveform1Dto2D( 

187 maps1D_to_2D: Tuple[np.ndarray, np.ndarray], waveform: np.ndarray, waveform2D: np.ndarray = None 

188) -> np.ndarray: 

189 """Get the 2D array representation of waveform 

190 

191 If waveform2D is passed, the values of waveform2D will be updated with `waveform`'s. 

192 Otherwise a new 2D array will be created. 

193 

194 Parameters 

195 ---------- 

196 maps1D_to_2D : tuple of np.ndarray 

197 The tuple holding the indices to go from 1D to 2D representation 

198 waveform : np.ndarray 

199 Waveform values in 1D shape. 

200 waveform2D : np.ndarray, optionnal 

201 An already existing 2D representation of the waveform, to update with `waveform`'s values. 

202 

203 Returns 

204 ------- 

205 np.ndarray 

206 A 2D array representing the waveform. (The array is independent of waveform, not a view) 

207 """ 

208 # Initialize waveform2D it with 0s if needed. 

209 if waveform2D is None: 

210 waveform2D = np.zeros( 

211 waveform.shape[:-1] + (maps1D_to_2D[0].max() + 1, maps1D_to_2D[1].max() + 1), dtype=waveform.dtype 

212 ) 

213 

214 waveform2D[..., *maps1D_to_2D] = waveform 

215 return waveform2D 

216 

217 

218def waveform2Dto1D(maps1D_to_2D: np.ndarray, waveform2D: np.ndarray) -> np.ndarray: 

219 """Get the 1D array representing the waveform from the 2D representation `waveform2D`. 

220 

221 Notes 

222 ----- 

223 The result is a view in `waveform2D`! Modifying the view will modify waveform2D! 

224 

225 Parameters 

226 ---------- 

227 maps1D_to_2D : tuple of np.ndarray 

228 The tuple holding the indices to go from 2D to 1D representation 

229 waveform2D : np.ndarray 

230 The 2D array holding the waveform values. 

231 

232 Returns 

233 ------- 

234 np.ndarray 

235 1D array holding the waveform values. 

236 """ 

237 return np.ascontiguousarray(waveform2D[..., *maps1D_to_2D]) 

238 

239 

240def neighbors_only_stencil() -> np.ndarray: 

241 """Return the stencil selecting __only the neighbors__ of a pixel in 2D array. 

242 

243 The pixel itself is not included: center element of the stencil is 0. 

244 

245 Notes 

246 ----- 

247 The stencil values depend on the way the 1D to 2D conversion is performed. Depending on how the axis are deformed, 

248 it could be transposed or reversed. The current implementation does 

249 0 1 1 4 

250 2 3 4 -> 0 3 6 

251 5 6 2 5 

252 so the stencil is 1 where the neighbors are and 0 otherwise (and 0 at the center to exclude current pixel). 

253 

254 """ 

255 return np.array([[1, 1, 0], [1, 0, 1], [0, 1, 1]], dtype=bool) 

256 

257 

258def leakage_pixel_masks(pixel_positions: np.ndarray) -> np.ndarray: 

259 """Returns a mask (boolean array) that multiplied with waveforms (1D) puts all pixels except the outer rings to 0. 

260 

261 Parameters 

262 ---------- 

263 pixel_positions : np.ndarray 

264 2D array (shape: (2, N_pixels)) containing the pixels x and y coordinates. This should 

265 be the actual pixels positions in the camera. It is important that the referential in 

266 which the position are measured has equal metrics on both axis (1m in the real world 

267 is 1 on x _and_ y axis) 

268 

269 Returns 

270 ------- 

271 leakage_mask: np.ndarray 

272 Mask array with values True at the indices of pixels on the outermost rings, False otherwise. 

273 The shape is (2, nb_pixels). leakage_mask[0, :] selects the pixels of the outermost ring (leakage 1) 

274 while leakage[1:] selects the pixels of the 1st and 2nd outermost ring (leakage 2). 

275 """ 

276 neighbors_indices = _get_neighbors_indices(pixel_positions) 

277 # leakage 1 pixels are the one of the borders, so they have less than 6 neighbors. 

278 # we use the fact that the neighbors_indices array has invalid indices for non-existing neighbors. 

279 leakage_1_mask = (neighbors_indices >= pixel_positions.shape[1]).any(axis=1) 

280 # leakage 2 pixels are the ones that are neighbors of leakage 1 pixels, but are not in leakage 1 themselves. 

281 # find them by getting the indices of leakage 1 pixels with nonzero, then use isin to see if there are neighbors 

282 # finally exclude the leakage 1 pixels 

283 leakage_2_mask = np.isin(neighbors_indices, np.nonzero(leakage_1_mask)[0]).any(axis=1) & np.bitwise_not( 

284 leakage_1_mask 

285 ) 

286 return np.stack([leakage_1_mask, leakage_1_mask | leakage_2_mask], axis=0)