updated Path

openptv_python/calibration.py

@@ -1,7 +1,7 @@
 """Calibration data structures and functions."""
 
 import copy
-import pathlib
+from pathlib import Path
 from typing import Optional
 
 import numpy as np
@@ -127,7 +127,7 @@ def __init__(self,
 
 
     @classmethod
-    def from_file(cls, ori_file: str, add_file: str | None):
+    def from_file(cls, ori_file: Path, add_file: Path | None):
         """
         Read exterior and interior orientation, and if available, parameters for distortion corrections.
 
@@ -141,7 +141,7 @@ def from_file(cls, ori_file: str, add_file: str | None):
         -------
         - ext_par, int_par, glass, addp: Calibration object parts without multimedia lookup table.
         """
-        if not pathlib.Path(ori_file).exists():
+        if not ori_file.exists():
             raise IOError(f"File {ori_file} does not exist")
 
         ret = cls()
@@ -166,6 +166,8 @@ def from_file(cls, ori_file: str, add_file: str | None):
         # this is anyhow default
         # self.mmlut.data = None  # no multimedia data yet
 
+        ret.added_par = np.array([0,0,0,0,0,1,0], dtype=np.float64)
+
         # Additional parameters
         if add_file is not None:
             with open(add_file, "r", encoding="utf-8") as fp:
@@ -179,10 +181,6 @@ def from_file(cls, ori_file: str, add_file: str | None):
         else:
             # print("no addpar fallback used")  # Waits for proper logging.
             print("No addpar file found. Using default values for radial distortion")
-            # ret.added_par.k1 = ret.added_par.k2 = ret.added_par.k3 \
-            #     = ret.added_par.p1 = ret.added_par.p2 = ret.added_par.she = 0.0
-            # ret.added_par.scx = 1.0
-            ret.added_par = np.array([0,0,0,0,0,1,0], dtype=np.float64)
 
         return ret
         # print(f"Calibration data read from files {ori_file} and {add_file}")
@@ -395,7 +393,7 @@ def write_ori(
     ext_par: np.recarray,
     int_par: np.recarray,
     glass: np.ndarray,
-    added_par: np.recarray,
+    added_par: np.ndarray,
     filename: str,
     add_file: Optional[str],
 ) -> bool:
@@ -424,7 +422,7 @@ def write_ori(
     return success
 
 
-def read_ori(ori_file: str, add_file: str) -> Calibration:
+def read_ori(ori_file: Path, add_file: Path) -> Calibration:
     """
     Read exterior and interior orientation, and if available, parameters for distortion corrections.
 
@@ -495,7 +493,7 @@ def compare_addpar(a1, a2):
     return np.array_equal(a1, a2)
 
 
-def read_calibration(ori_file: str, addpar_file: str) -> Calibration:
+def read_calibration(ori_file: Path, addpar_file: Path | None) -> Calibration:
     """Read the orientation file including the added parameters."""
     return Calibration().from_file(ori_file, addpar_file)
 

openptv_python/parameters.py

@@ -1,5 +1,4 @@
 """Parameters for OpenPTV-Python."""
-import os
 from dataclasses import asdict, dataclass, field
 from pathlib import Path
 from typing import List, Tuple
@@ -146,9 +145,9 @@ def get_last(self):
         return self.last
 
     @classmethod
-    def from_file(cls, filename: str, num_cams: int):
+    def from_file(cls, filename: Path, num_cams: int):
         """Read sequence parameters from file."""
-        if not Path(filename).exists():
+        if not filename.exists():
             raise IOError("File {filename} does not exist.")
 
         ret = cls()
@@ -162,7 +161,7 @@ def from_file(cls, filename: str, num_cams: int):
         return ret
 
 
-def read_sequence_par(filename: str, num_cams: int = TR_MAX_CAMS) -> SequencePar:
+def read_sequence_par(filename: Path, num_cams: int = TR_MAX_CAMS) -> SequencePar:
     """Read sequence parameters from file and return SequencePar object."""
     return SequencePar().from_file(filename, num_cams)
 
@@ -213,7 +212,7 @@ class TrackPar(Parameters):
     #     }
 
     @classmethod
-    def from_file(cls, filename: str):
+    def from_file(cls, filename: Path):
         """Read tracking parameters from file and return TrackPar object.
 
         Note that the structure has 13 attributes, from which we read only 9
@@ -306,7 +305,7 @@ def get_dny(self):
         return self.dny
 
 
-def read_track_par(filename: str) -> TrackPar:
+def read_track_par(filename: Path) -> TrackPar:
     """Read tracking parameters from file and return TrackPar object."""
     return TrackPar().from_file(filename)
 
@@ -377,7 +376,7 @@ def set_corrmin(self, corrmin: float):
         self.corrmin = corrmin
 
     @classmethod
-    def from_file(cls, filename: str):
+    def from_file(cls, filename: Path):
         """Read volume parameters from file.
 
         Args:
@@ -401,7 +400,7 @@ def from_file(cls, filename: str):
         return cls(x_lay, z_min_lay, z_max_lay, cn, cnx, cny, csumg, eps0, corrmin)
 
 
-def read_volume_par(filename: str) -> VolumePar:
+def read_volume_par(filename: Path) -> VolumePar:
     """Read volume parameters from file and returns volume_par object.
 
     Args:
@@ -497,10 +496,10 @@ def get_tiff_flag(self):
         return self.tiff_flag
 
     @classmethod
-    def from_file(cls, filename: str):
+    def from_file(cls, filename: Path):
         """Read control parameters from file and return ControlPar object."""
         ret = cls()
-        if not os.path.isfile(filename):
+        if not filename.exists():
             raise FileNotFoundError(f"Could not open file {filename}")
 
         with open(filename, "r", encoding="utf-8") as par_file:
@@ -546,7 +545,7 @@ def to_dict(cls, data):
         return control_par_dict
 
 
-def read_control_par(filename: str) -> ControlPar:
+def read_control_par(filename: Path) -> ControlPar:
     """Read control parameters from file and return ControlPar object."""
     return ControlPar().from_file(filename)
 
@@ -608,7 +607,7 @@ class TargetPar(Parameters):
     #     }
 
     @classmethod
-    def from_file(cls, filename: str):
+    def from_file(cls, filename: Path):
         """Read target parameters from file and returns target_par object.
 
         Reads target recognition parameters from a legacy detect_plate.par file,
@@ -673,7 +672,7 @@ def get_min_sum_grey(self):
         """Return the sum grey bounds."""
         return self.sumg_min
 
-def read_target_par(filename: str) -> TargetPar:
+def read_target_par(filename: Path) -> TargetPar:
     """Read target parameters from file and returns target_par object."""
     tpar = TargetPar()
     return tpar.from_file(filename)
@@ -712,7 +711,7 @@ class OrientPar(Parameters):
     interfflag: int = 0
 
     @classmethod
-    def from_file(cls, filename: str):
+    def from_file(cls, filename: Path):
         """Read orientation parameters from file and returns orient_par object."""
         ret = cls()
         try:
@@ -777,7 +776,7 @@ def from_file(cls, file_path: str, num_cams: int):
         return cls(fixp_name, img_name, img_ori0, tiff_flag, pair_flag, chfield)
 
 
-def read_cal_ori_parameters(file_path: str, num_cams: int) -> CalibrationPar:
+def read_cal_ori_parameters(file_path: Path, num_cams: int) -> CalibrationPar:
     """Read from cal_ori.par file."""
     with open(file_path, 'r', encoding="utf-8") as file:
         fixp_name = file.readline().strip()
@@ -799,7 +798,7 @@ class MultiPlanesPar(Parameters):
     filename: list = field(default_factory=list)
 
     @classmethod
-    def from_file(cls, file_path: str):
+    def from_file(cls, file_path: Path):
         """Read from multiplanes.par file."""
         with open(file_path, 'r', encoding="utf-8") as file:
             num_planes = int(file.readline().strip())
@@ -814,14 +813,14 @@ class ExaminePar(Parameters):
     combine_flag: bool = False
 
     @classmethod
-    def from_file(cls, file_path: str):
+    def from_file(cls, file_path: Path):
         """Read from examine.par file."""
         with open(file_path, 'r', encoding="utf-8") as file:
             examine_flag = bool(int(file.readline().strip()))
             combine_flag = bool(int(file.readline().strip()))
         return cls(examine_flag, combine_flag)
 
-def read_examine_par(file_path: str) -> ExaminePar:
+def read_examine_par(file_path: Path) -> ExaminePar:
     """Read from examine.par file."""
     with open(file_path, 'r', encoding="utf-8") as file:
         examine_flag = bool(int(file.readline().strip()))
@@ -835,14 +834,14 @@ class PftVersionPar(Parameters):
     existing_target_flag: bool = False
 
     @classmethod
-    def from_file(cls, file_path: str):
+    def from_file(cls, file_path: Path):
         """Read from pft_version.par file."""
         with open(file_path, 'r', encoding="utf-8") as file:
             pft_version = bool(int(file.readline().strip()))
         return cls(pft_version)
 
     @classmethod
-    def write(cls, file_path: str):
+    def write(cls, file_path: Path):
         """Write to pft_version.par file."""
         with open(file_path, 'w', encoding="utf-8") as file:
             file.write(f"{cls.existing_target_flag}\n")

openptv_python/sortgrid.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 from typing import List
 
 import numpy as np
@@ -119,7 +120,7 @@ def read_sortgrid_par(filename) -> int:
     return eps
 
 
-def read_calblock(filename: str) -> np.recarray: #List[Coord3d]:
+def read_calblock(filename: Path) -> np.recarray: #List[Coord3d]:
     """
     Read the calibration block file into the structure of 3D positions and pointers.
 

openptv_python/tracking_frame_buf.py

@@ -1,6 +1,7 @@
 """Tracking frame buffer."""
 from collections import deque
 from dataclasses import dataclass, field
+from pathlib import Path
 from typing import Deque, List, Tuple
 
 import numpy as np
@@ -172,10 +173,11 @@ def read_targets(file_base: str, frame_num: int) -> List[Target]:
 
     if frame_num > 0:
         # filename = f"{file_base}{frame_num:04d}_targets"
-        filename = file_base % frame_num + '_targets'
+        fname = file_base % frame_num + '_targets'
     else:
-        filename = f"{file_base}_targets"
+        fname = f"{file_base}_targets"
 
+    filename = Path(fname)
     print(f" filename: {filename}")
 
     try:

openptv_python/tracking_run.py

@@ -1,6 +1,7 @@
 """Tracking run module."""
 import math
 from dataclasses import dataclass
+from pathlib import Path
 from typing import List
 
 from openptv_python.calibration import Calibration
@@ -97,10 +98,10 @@ def __init__(
 
 
 def tr_new(
-    seq_par_fname: str,
-    tpar_fname: str,
-    vpar_fname: str,
-    cpar_fname: str,
+    seq_par_fname: Path,
+    tpar_fname: Path,
+    vpar_fname: Path,
+    cpar_fname: Path,
     buf_len: int,
     max_targets: int,
     corres_file_base: str,

tests/gen_track_data.py

@@ -4,6 +4,7 @@
 testing. It starts from (0,0,0) and moves in a straight line on the x axis,
 at a slow velocity.
 """
+from pathlib import Path
 from typing import List
 
 import numpy as np
@@ -21,16 +22,16 @@
 part_traject[:, 0] = np.r_[:num_frames] * velocity
 
 # Find targets on each camera.
-cpar = ControlPar(num_cams=3).from_file("testing_fodder/track/parameters/control_newpart.par")
+cpar = ControlPar(num_cams=3).from_file(Path("tests/testing_fodder/track/parameters/control_newpart.par"))
 
 targs: List[List[List[float]]] = [
     [[0.0, 0.0] for _ in range(num_frames)] for _ in range(num_cams)
 ]
 
 for cam in range(num_cams):
     cal = Calibration().from_file(
-        f"testing_fodder/cal/sym_cam{cam+1}.tif.ori",
-        "testing_fodder/cal/cam1.tif.addpar",
+        Path(f"tests/testing_fodder/cal/sym_cam{cam+1}.tif.ori"),
+        Path("tests/testing_fodder/cal/cam1.tif.addpar"),
     )
     # check this out
     for frame in range(num_frames):
@@ -41,7 +42,7 @@
 for frame in range(num_frames):
     # write 3D positions:
     with open(
-        f"testing_fodder/track/res_orig/particles.{frame+1}", "w", encoding="utf-8"
+        f"tests/testing_fodder/track/res_orig/particles.{frame+1}", "w", encoding="utf-8"
     ) as outfile:
         # Note correspondence to the single target in each frame.
         outfile.writelines(
@@ -63,7 +64,7 @@
     # write associated targets from all cameras:
     for cam in range(num_cams):
         with open(
-            f"testing_fodder/track/newpart/cam{cam+1}.{frame+1:04d}_targets",
+            f"tests/testing_fodder/track/newpart/cam{cam+1}.{frame+1:04d}_targets",
             "w",
             encoding="utf-8",
         ) as outfile:

tests/test_burgers.py

@@ -58,7 +58,7 @@ def read_all_calibration(num_cams: int = 4) -> list[Calibration]:
     for cam in range(num_cams):
         ori_name = ori_tmpl % (cam + 1)
         added_name = added_tmpl % (cam + 1)
-        calib.append(read_calibration(ori_name, added_name))
+        calib.append(read_calibration( Path(ori_name), Path(added_name) ))
 
     return calib
 
@@ -71,6 +71,7 @@ def test_burgers(self):
         current_directory = Path.cwd()
         print(f"working from {current_directory}")
         directory = Path("tests/testing_fodder/burgers")
+        parameters_path = (directory / "parameters").resolve(strict=True)
 
         os.chdir(directory)
 
@@ -86,7 +87,7 @@ def test_burgers(self):
         copy_directory("res_orig/", "res/")
         copy_directory("img_orig/", "img/")
 
-        cpar = read_control_par("parameters/ptv.par")
+        cpar = read_control_par(parameters_path / "ptv.par")
         self.assertIsNotNone(cpar)
 
         calib = read_all_calibration(cpar.num_cams)
@@ -95,10 +96,10 @@ def test_burgers(self):
         print("Test Burgers vortex case")
 
         run = tr_new(
-            "parameters/sequence.par",
-            "parameters/track.par",
-            "parameters/criteria.par",
-            "parameters/ptv.par",
+            parameters_path / "sequence.par",
+            parameters_path / "track.par",
+            parameters_path / "criteria.par",
+            parameters_path / "ptv.par",
             4,
             20000,
             "res/rt_is",
@@ -124,10 +125,10 @@ def test_burgers(self):
             run.nlinks, 17, f"Was expecting nlinks == 17 but found {run.nlinks}")
 
         run = tr_new(
-            "parameters/sequence.par",
-            "parameters/track.par",
-            "parameters/criteria.par",
-            "parameters/ptv.par",
+            parameters_path / "sequence.par",
+            parameters_path / "track.par",
+            parameters_path / "criteria.par",
+            parameters_path / "ptv.par",
             4,
             20000,
             "res/rt_is",