numpy recarrays work

Author: alexlib

openptv_python/correspondences.py

@@ -4,7 +4,14 @@
 import numpy as np
 
 from .calibration import Calibration
-from .constants import COORD_UNUSED, CORRES_NONE, MAX_TARGETS, MAXCAND, NMAX, PT_UNUSED
+from .constants import (
+    COORD_UNUSED,
+    CORRES_NONE,
+    MAX_TARGETS,
+    MAXCAND,
+    NMAX,
+    PT_UNUSED,
+)
 from .epi import epi_mm
 from .find_candidate import find_candidate
 from .parameters import ControlPar, VolumePar
@@ -44,8 +51,8 @@ def __init__(self, targs, cpar, cal, tol=0.00001, reset_numbers=True):
             don't.
         """
         self._num_pts = len(targs)
-        self.buf = np.empty(self._num_pts, \
-            dtype=np.dtype([('x', np.float64), ('y', np.float64), ('pnr', np.int32)]))
+        self.buf = np.empty(self._num_pts,
+                            dtype=np.dtype([('x', np.float64), ('y', np.float64), ('pnr', np.int32)]))
 
         for tnum, targ in enumerate(targs):
             targ = targs[tnum]
@@ -57,7 +64,7 @@ def __init__(self, targs, cpar, cal, tol=0.00001, reset_numbers=True):
 
             self.buf[tnum]['x'], self.buf[tnum]['y'] = dist_to_flat(
                 self.buf[tnum]['x'], self.buf[tnum]['y'], cal, tol
-                )
+            )
             self.buf[tnum]['pnr'] = targ.pnr
 
         self.buf.sort(order='x')
@@ -100,16 +107,17 @@ def __del__(self):
 
 
 Correspond_dtype = np.dtype([
-    ('p1', np.int32), # PT_UNUSED
-    ('n', np.int32), # 0
-    ('p2', (np.int32, MAXCAND)), # np.zeros
-    ('corr', (np.float64, MAXCAND)), # np.zeros
-    ('dist', (np.float64, MAXCAND)) # np.zeros
+    ('p1', np.int32),  # PT_UNUSED
+    ('n', np.int32),  # 0
+    ('p2', (np.int32, MAXCAND)),  # np.zeros
+    ('corr', (np.float64, MAXCAND)),  # np.zeros
+    ('dist', (np.float64, MAXCAND))  # np.zeros
 ])
 
+
 def safely_allocate_target_usage_marks(
     num_cams: int, nmax: int = NMAX
-) -> np.ndarray: # num_cams x nmax instead of List[List[int]]:
+) -> np.ndarray:  # num_cams x nmax instead of List[List[int]]:
     """Allocate space for per-camera arrays marking whether a certain target was used.
 
     If some allocation failed, it cleans up memory and returns NULL. Allocated arrays are zeroed
@@ -134,6 +142,7 @@ def safely_allocate_target_usage_marks(
 
     return np.zeros((num_cams, nmax), dtype=np.int32)
 
+
 def safely_allocate_adjacency_lists(
     num_cams: int, target_counts: List[int]
 ) -> np.recarray:
@@ -148,7 +157,8 @@ def safely_allocate_adjacency_lists(
         #     for c1 in range(num_cams)
         # ]
 
-        lists = np.recarray((num_cams, num_cams, max(target_counts)),dtype=Correspond_dtype)
+        lists = np.recarray((num_cams, num_cams, max(
+            target_counts)), dtype=Correspond_dtype)
 
     except MemoryError as exc:
         raise MemoryError("Failed to allocate adjacency lists.") from exc
@@ -160,9 +170,9 @@ def safely_allocate_adjacency_lists(
     lists.corr = np.zeros(MAXCAND)
     lists.dist = np.zeros(MAXCAND)
 
-
     return lists
 
+
 def four_camera_matching(
     corr_list: np.recarray,
     base_target_count,
@@ -240,7 +250,7 @@ def four_camera_matching(
 
 
 def three_camera_matching(
-    corr_list: np.recarray, # num_cam, num_cam, num_targets
+    corr_list: np.recarray,  # num_cam, num_cam, num_targets
     num_cams,
     target_counts,
     accept_corr,
@@ -345,7 +355,8 @@ def consistent_pair_matching(
                 if p2 >= nmax or tusage[i2][p2] > 0:
                     continue
 
-                corr = corr_list[i1][i2][i].corr[0] / corr_list[i1][i2][i].dist[0]
+                corr = corr_list[i1][i2][i].corr[0] / \
+                    corr_list[i1][i2][i].dist[0]
                 if corr <= accept_corr:
                     continue
 
@@ -365,8 +376,8 @@ def consistent_pair_matching(
 
 
 def match_pairs(
-    corr_lists: np.recarray, # num_cam, num_cam, num_targets
-    corrected: np.recarray, # List[List[Coord2d]],
+    corr_lists: np.recarray,  # num_cam, num_cam, num_targets
+    corrected: np.recarray,  # List[List[Coord2d]],
     frm: Frame,
     vpar: VolumePar,
     cpar: ControlPar,
@@ -466,7 +477,8 @@ def match_pairs(
 
 
 def take_best_candidates(
-    src: np.recarray, dst: np.recarray, num_cams: int, tusage: np.ndarray #List[n_tupel]
+    # List[n_tupel]
+    src: np.recarray, dst: np.recarray, num_cams: int, tusage: np.ndarray
 ):
     """
     Take the best candidates from the candidate list based on their correlation measure.
@@ -509,8 +521,8 @@ def take_best_candidates(
     taken = 0
 
     # Sort candidates by match quality (.corr)
-    src.sort(order='corr') # by corr
-    src = src[::-1] # reverse order
+    src.sort(order='corr')  # by corr
+    src = src[::-1]  # reverse order
 
     # Take candidates from the top to the bottom of the sorted list
     # Only take if none of the corresponding targets have been used
@@ -613,7 +625,8 @@ def py_correspondences(
         frm.targets[cam] = img_pts[cam]
 
     # The biz:
-    corresp_buf = correspondences(frm, flat_coords, vparam, cparam, calib, match_counts)
+    corresp_buf = correspondences(
+        frm, flat_coords, vparam, cparam, calib, match_counts)
 
     # Distribute data to return structures:
     # sorted_pos = [None] * (num_cams - 1)
@@ -623,9 +636,12 @@ def py_correspondences(
     last_count = 0
 
     for clique_type in range(num_cams - 1):
-        num_points = match_counts[4 - num_cams + clique_type]  # for 1-4 cameras
-        clique_targs = np.full((num_cams, num_points, 2), PT_UNUSED, dtype=np.float64)
-        clique_ids = np.full((num_cams, num_points), CORRES_NONE, dtype=np.int_)
+        num_points = match_counts[4 - num_cams +
+                                  clique_type]  # for 1-4 cameras
+        clique_targs = np.full((num_cams, num_points, 2),
+                               PT_UNUSED, dtype=np.float64)
+        clique_ids = np.full((num_cams, num_points),
+                             CORRES_NONE, dtype=np.int_)
 
         # Trace back the pixel target properties through the flat metric
         # intermediary that's x-sorted.
@@ -662,7 +678,7 @@ def correspondences(
     cpar: ControlPar,
     calib: List[Calibration],
     match_counts: List[int],
-) -> np.recarray: # n_tupel_dtype
+) -> np.recarray:  # n_tupel_dtype
     """Find correspondences between cameras.
 
     /*  correspondences() generates a list of tuple target numbers (one for each
@@ -699,8 +715,13 @@ def correspondences(
     nmax = NMAX
 
     # Allocation of scratch buffers for internal tasks and return-value space
-    con0 = np.recarray((nmax * cpar.num_cams), dtype=n_tupel_dtype)
-    con = np.recarray((nmax * cpar.num_cams), dtype=n_tupel_dtype)
+    con0 = np.recarray((nmax * cpar.num_cams,), dtype=n_tupel_dtype)
+    con0.p = 0
+    con0.corr = 0.0
+
+    con = np.recarray((nmax * cpar.num_cams,), dtype=n_tupel_dtype)
+    con.p = 0
+    con.corr = 0.0
 
     tim = safely_allocate_target_usage_marks(cpar.num_cams, nmax)
 
@@ -732,7 +753,7 @@ def correspondences(
         )
 
         match_counts[1] = take_best_candidates(
-            con0, con[match_counts[3] :], cpar.num_cams, tim
+            con0, con[match_counts[3]:], cpar.num_cams, tim
         )
         match_counts[3] += match_counts[1]
 
@@ -742,7 +763,7 @@ def correspondences(
             corr_list, cpar.num_cams, frm.num_targets, vpar.corrmin, con0, 4 * nmax, tim
         )
         match_counts[2] = take_best_candidates(
-            con0, con[match_counts[3] :], cpar.num_cams, tim
+            con0, con[match_counts[3]:], cpar.num_cams, tim
         )
         match_counts[3] += match_counts[2]
 
@@ -766,7 +787,7 @@ def correspondences(
 
 
 def single_cam_correspondences(
-    img_pts: List[Target], corrected: np.recarray #List[Coord2d]
+    img_pts: List[Target], corrected: np.recarray  # List[Coord2d]
 ) -> Tuple[List[np.ndarray], List[np.ndarray], int]:
     """
     Single camera correspondence is not a real correspondence, it will be only a projection.

openptv_python/find_candidate.py

@@ -145,7 +145,8 @@ def find_candidate(
         # cand.append(Candidate(pnr=j, tol=d, corr=corr))
         cand.append(np.array([(j, d, corr)], dtype=Candidate_dtype)) # type: ignore
 
-        out = np.array(cand).view(np.recarray).flatten()
+
+    out = np.array(cand).view(np.recarray).flatten()
         # print(f"appended: {cand[-1]}")
 
     return out # type: ignore

openptv_python/track.py

@@ -23,7 +23,7 @@
 from .imgcoord import img_coord
 from .orientation import point_position
 from .parameters import ControlPar, SequencePar, TrackPar, VolumePar
-from .tracking_frame_buf import Corres_dtype, Frame, Pathinfo, Target
+from .tracking_frame_buf import Frame, Pathinfo, Target
 from .tracking_run import TrackingRun
 from .trafo import dist_to_flat, metric_to_pixel, pixel_to_metric
 from .vec_utils import vec_copy, vec_diff_norm, vec_subt
@@ -760,8 +760,8 @@ def add_particle(frm: Frame, pos: np.ndarray, cand_inds: np.ndarray) -> None:
     else:
         ref_path_inf = Pathinfo()
         frm.path_info.append(ref_path_inf)
-
-        frm.correspond.append(np.recarray((1,), dtype=Corres_dtype))
+        frm.correspond = np.resize(frm.correspond, frm.correspond.shape[0] + 1).view(np.recarray)
+        ref_corres = frm.correspond.view(np.recarray)
 
     ref_path_inf.x = vec_copy(pos)
     ref_path_inf.reset_links()

openptv_python/tracking_frame_buf.py

@@ -15,6 +15,7 @@
     PREV_NONE,
     PRIO_DEFAULT,
     PT_UNUSED,
+    TR_UNUSED,
 )
 from .epi import Coord2d_dtype
 from .parameters import ControlPar
@@ -26,7 +27,7 @@
 ])
 
 
-def quicksort_n_tupel(arr: np.ndarray) -> np.ndarray:
+def quicksort_n_tupel(arr: np.recarray) -> np.recarray:
     """
     Quicksorts a list of n_tupel instances based on the corr attribute.
 
@@ -40,7 +41,9 @@ def quicksort_n_tupel(arr: np.ndarray) -> np.ndarray:
     -------
       A list of n_tupel instances, sorted by the corr attribute.
     """
-    return np.sort(arr, order="corr")
+    # inline sorting
+    arr.sort(order="corr")
+    return arr
 
 
 
@@ -56,7 +59,7 @@ def quicksort_n_tupel(arr: np.ndarray) -> np.ndarray:
     #     return self.nr == other.nr and np.all(self.p == other.p)
 
 
-def compare_corres(c1: np.ndarray, c2: np.ndarray) -> bool:
+def compare_corres(c1: np.recarray, c2: np.recarray) -> bool:
     """
     Compare two Corres instances.
 
@@ -69,7 +72,7 @@ def compare_corres(c1: np.ndarray, c2: np.ndarray) -> bool:
     -------
         True if the Corres instances are equal, False otherwise.
     """
-    return np.array_equal(c1, c2)
+    return (c1 == c2).all()
 
 
 @dataclass
@@ -317,7 +320,9 @@ def __init__(self, num_cams: int, max_targets: int = MAX_TARGETS):
         """
         self.path_info = [Pathinfo() for _ in range(max_targets)]
 
-        self.correspond = [np.recarray((1,), dtype=Corres_dtype) for _ in range(max_targets)]
+        self.correspond = np.recarray((max_targets), dtype=Corres_dtype)
+        self.correspond.p = TR_UNUSED
+        self.correspond.nr = 0
 
         self.targets = [[Target() for _ in range(max_targets)] for _ in range(num_cams)]
         # self.targets = [[] for _ in range(num_cams)]
@@ -689,7 +694,7 @@ def read_path_frame(
     linkage_file_base: str,
     prio_file_base: str,
     frame_num: int,
-) -> Tuple[List[np.recarray], List[Pathinfo]]: #List[Corres]
+) -> Tuple[np.recarray, List[Pathinfo]]: #List[Corres]
     """Read a rt_is frames from the disk.
 
         /* Reads rt_is files. these files contain both the path info and the
@@ -719,14 +724,14 @@ def read_path_frame(
         filein = open(fname, "r", encoding="utf-8")
     except IOError:
         print(f"Can't open ascii file: {fname}")
-        return [np.recarray(0,dtype=Corres_dtype)], []
+        return np.recarray(0, dtype=Corres_dtype), []
 
     # we do not need number of particles, reading till EOF
     n_particles = int(filein.readline())
     # print(f"Reading {n_particles} particles from {fname}")
     # cor_buf = [Corres() for _ in range(n_particles)] # we do not want empty lists
 
-    cor_buf = [np.recarray((0,), dtype=Corres_dtype) for _ in range(n_particles)] # we do not want empty lists
+    cor_buf = np.recarray((n_particles), dtype=Corres_dtype) # we do not want empty lists
 
     path_buf = [Pathinfo() for _ in range(n_particles)]
 
@@ -736,7 +741,7 @@ def read_path_frame(
             linkagein = open(fname, "r", encoding="utf-8")
         except IOError:
             print(f"Can't open linkage file: {fname}")
-            return [np.recarray(0, dtype=Corres_dtype)], []
+            return np.recarray(0, dtype=Corres_dtype), []
 
         linkagein.readline()
     else:
@@ -748,7 +753,7 @@ def read_path_frame(
             prioin = open(fname, "r", encoding="utf-8")
         except IOError:
             print(f"Can't open prio file: {fname}")
-            return [], []
+            return np.recarray(0, dtype=Corres_dtype), []
 
         prioin.readline()
     else:
@@ -781,7 +786,7 @@ def read_path_frame(
 
         vals = np.fromstring(line, dtype=float, sep=" ")
         cor_buf[targets].nr = targets + 1
-        cor_buf[targets].p = vals[-4:].astype(int).tolist()
+        cor_buf[targets].p = vals[-4:].astype(int)
         path_buf[targets].x = vals[1:-4]
 
         # print(cor_buf[targets].nr, cor_buf[targets].p, path_buf[targets].x)
@@ -798,7 +803,7 @@ def read_path_frame(
 
 
 def write_path_frame(
-    cor_buf: List[np.recarray], #List[Corres],
+    cor_buf: np.recarray, #List[Corres],
     path_buf: List[Pathinfo],
     num_parts: int,
     corres_file_base: str,