Merge remote-tracking branch 'origin/develop'

ANP-Granular · Oct 4, 2024 · 5412b25 · 5412b25
2 parents f06fa4b + 95dfbfa
commit 5412b25
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diff --git a/.github/workflows/code_style.yml b/.github/workflows/code_style.yml
@@ -16,7 +16,7 @@ jobs:
     continue-on-error: true
     strategy:
       matrix:
-        python_version: ['3.11']
+        python_version: ['3.12']
     steps:
         - uses: actions/checkout@v4
         - name: Set up Python ${{ matrix.python_version }}

diff --git a/.github/workflows/publish_particledetection.yml b/.github/workflows/publish_particledetection.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
         matrix:
-          python_version: ['3.11']
+          python_version: ['3.12']
     steps:
       - uses: actions/checkout@v4
         with:

diff --git a/.github/workflows/publish_rodtracker.yml b/.github/workflows/publish_rodtracker.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
         matrix:
-          python_version: ['3.11']
+          python_version: ['3.12']
     steps:
       - uses: actions/checkout@v4
         with:

diff --git a/ParticleDetection/CHANGELOG.md b/ParticleDetection/CHANGELOG.md
@@ -1,7 +1,19 @@
 ## [Unreleased]
+
+## [v0.4.3]
+### Fixed
+- tracking now works as intended ([#96](https://github.com/ANP-Granular/ParticleTracking/issues/96))
+- tracking/matching tests were updated according to the fixed tracking issue 
+
+## [v0.4.2]
 ### Added
 - support for Python 3.12
 
+### Fixed
+- error mitigation for failed projection error binning
+- numpy version mismatch ([#90](https://github.com/ANP-Granular/ParticleTracking/issues/90))
+- minimum test coverage
+
 ## [v0.4.1]
 ### Added
 - support for python3.11
@@ -51,7 +63,8 @@
 ### Added
 - start versioning
 
-[Unreleased]: https://github.com/ANP-Granular/ParticleTracking/compare/v0.4.1+ParticleTracking...HEAD
+[Unreleased]: https://github.com/ANP-Granular/ParticleTracking/compare/v0.4.2+ParticleTracking...HEAD
+[v0.4.2]: https://github.com/ANP-Granular/ParticleTracking/compare/v0.4.1+ParticleTracking...v0.4.2+ParticleTracking
 [v0.4.1]: https://github.com/ANP-Granular/ParticleTracking/compare/v0.4.0+ParticleTracking...v0.4.1+ParticleTracking
 [v0.4.0]: https://github.com/ANP-Granular/ParticleTracking/compare/v0.3.1+ParticleTracking...v0.4.0+ParticleTracking
 [v0.3.1]: https://github.com/ANP-Granular/ParticleTracking/compare/v0.3.1+ParticleTracking
diff --git a/...articleDetection/reconstruct_3D/example_calibration/Matlab/world_transformation_gp12.json b/...articleDetection/reconstruct_3D/example_calibration/Matlab/world_transformation_gp12.json
@@ -0,0 +1,24 @@
+{
+  "rotation": [
+    [
+      1.0425226613259928,
+      -0.0004143987226463844,
+      -0.006185995129884015
+    ],
+    [
+      -0.010958551087494509,
+      -0.9981086439453789,
+      -0.009663203036154984
+    ],
+    [
+      -0.0001673295899603522,
+      0.0055522462000225925,
+      -1.0051994470916754
+    ]
+  ],
+  "translation": [
+    4.032122379281649,
+    -1.8661071654922172,
+    283.13110014701454
+  ]
+}
diff --git a/...ibration/Matlab/world_transformation.json → ...rld_transformation_old_format_matlab.json b/...ibration/Matlab/world_transformation.json → ...rld_transformation_old_format_matlab.json
diff --git a/ParticleDetection/src/ParticleDetection/reconstruct_3D/matchND.py b/ParticleDetection/src/ParticleDetection/reconstruct_3D/matchND.py
@@ -342,6 +342,7 @@ def assign(
                 # Matching with a previous frame (+data) available
                 tmp_df, tmp_costs, tmp_lengths = match_frame(
                     data,
+                    tmp_df,
                     cam1_name,
                     cam2_name,
                     frame,
@@ -370,6 +371,7 @@ def assign(
 
 def match_frame(
     data: pd.DataFrame,
+    data_last_frame: pd.DataFrame,
     cam1_name: str,
     cam2_name: str,
     frame: int,
@@ -391,6 +393,8 @@ def match_frame(
     ----------
     data : DataFrame
         Dataset of rod positions.
+    data_last_frame : DataFrame
+        Dataset with updated rods data for the last frame.
     cam1_name : str
         First camera's identifier in the given dataset, e.g. ``"gp1"``.
     cam2_name : str
@@ -548,8 +552,9 @@ def match_frame(
 
     # TODO: check for NaN, so that an error is thrown, if NaNs encountered in
     # 3D coordinates
-    last_points = data.loc[
-        data.frame == frame - 1, ["x1", "y1", "z1", "x2", "y2", "z2"]
+    last_points = data_last_frame.loc[
+        data_last_frame.frame == frame - 1,
+        ["x1", "y1", "z1", "x2", "y2", "z2"],
     ]
     last_points = last_points.to_numpy()
     last_points = last_points.reshape((-1, 2, 3))

diff --git a/ParticleDetection/src/ParticleDetection/reconstruct_3D/visualization.py b/ParticleDetection/src/ParticleDetection/reconstruct_3D/visualization.py
@@ -169,8 +169,10 @@ def reprojection_errors_hist(reprojection_errors: np.ndarray) -> Figure:
             alpha=0.8,
             bins=np.arange(0, reprojection_errors.max(), 0.25),
         )
-    except ValueError as e:
-        if "Maximum allowed size exceeded" in str(e):
+    except Exception as e:
+        if ("Maximum allowed size exceeded" in str(e)) or (
+            "Unable to allocate" in str(e)
+        ):
             _logger.warning(f"{e}\nUsing a different binning strategy.")
             plt.hist(
                 reprojection_errors,

diff --git a/ParticleDetection/src/ParticleDetection/utils/data_conversions.py b/ParticleDetection/src/ParticleDetection/utils/data_conversions.py
@@ -236,7 +236,7 @@ def csv_split_by_frames(input_file: str, cut_frames: List[int]) -> List[str]:
         if len(next_slice) == 0:
             continue
         next_slice.reset_index(drop=True, inplace=True)
-        new_path = base_path + f"_{next_min}_{next_max-1}.csv"
+        new_path = base_path + f"_{next_min}_{next_max - 1}.csv"
         next_slice.to_csv(new_path, sep=",")
         written.append(new_path)
     return written

diff --git a/ParticleDetection/src/ParticleDetection/utils/helper_funcs.py b/ParticleDetection/src/ParticleDetection/utils/helper_funcs.py
@@ -610,10 +610,10 @@ def find_world_transform(
 
     transformations = {}
 
-    transformations["rot_comb"] = rot_comb.tolist()
-    transformations["trans_vec"] = trans_vec.tolist()
+    transformations["rotation"] = rot_comb.tolist()
+    transformations["translation"] = trans_vec.tolist()
 
     with open(out_json, "w") as fp:
-        json.dump(transformations, fp)
+        json.dump(transformations, fp, indent=2)
 
     return rot_comb, trans_vec
diff --git a/ParticleDetection/tests/test_reconstruct_3D/test_match_nd.py b/ParticleDetection/tests/test_reconstruct_3D/test_match_nd.py
@@ -94,7 +94,7 @@ def test_assign(tmp_path: Path):
 
 
 def test_match_frame_nd(example_data: pd.DataFrame):
-    frame = 508
+    frame = 507
     color = "black"
     calibration = dl.load_camera_calibration(EXAMPLES / "gp34.json")
     transformation = dl.load_world_transformation(
@@ -117,6 +117,7 @@ def test_match_frame_nd(example_data: pd.DataFrame):
     trans = transformation["translation"]
 
     result = mnd.match_frame(
+        example_data,
         example_data,
         "gp3",
         "gp4",

diff --git a/RodTracker/CHANGELOG.md b/RodTracker/CHANGELOG.md
@@ -1,4 +1,20 @@
-## [Unreleased]
+## [v0.6.4]
+
+### Added
+- missing sections in documentation were added (i.e. world coordinate transformation)
+- placeholders (TBDs) were replaced for API documentation 
+
+### Changed
+- default rod detection models (CPU and CUDA) are now published and downloaded via PyTorch Hub ([#102](https://github.com/ANP-Granular/ParticleTracking/issues/102))
+- default number of detected particles changed to 25 for each color (corresponding to default sample data)
+- ParticleDetection dependency updated (ParticleDetection v0.4.3 now required)
+- reverted to original dialogue window for stereo calibration/world transformation (for consistency with image loading dialogue)
+
+### Fixed
+- tracking now works as intended, previously it required to press the "solve" button frame by frame ([#96](https://github.com/ANP-Granular/ParticleTracking/issues/96))
+- solved issue when changes in data were not saved and reverted after pressing "solve" button 
+- tracking/matching tests were updated according to the fixed tracking issue 
+
 
 ## [v0.6.3]
 ### Added

diff --git a/RodTracker/pyproject.toml b/RodTracker/pyproject.toml
@@ -50,7 +50,7 @@ pandas= [
     {version = ">=2.1.1", python = ">=3.9"},
     {version = ">=1.2.5,<2.1", python = "<3.9"}
 ]
-ParticleDetection = ">=0.4.2.dev21"
+ParticleDetection = ">=0.4.3"
 platformdirs = ">=3.2.0"
 PyQt3D = ">=5.15.5"
 PyQt5 = ">=5.15.4"
@@ -108,7 +108,7 @@ files = [
 
 [tool.black]
 line-length = 79
-target-version = ['py38', 'py39', 'py310', 'py311']
+target-version = ['py38', 'py39', 'py310', 'py311', 'py312']
 extend-exclude = '''
 (
     .*mainwindow_layout..*

diff --git a/RodTracker/src/RodTracker/backend/detection.py b/RodTracker/src/RodTracker/backend/detection.py
@@ -14,7 +14,12 @@
 # You should have received a copy of the GNU General Public License
 # along with RodTracker. If not, see <http://www.gnu.org/licenses/>.
 
-"""**TBD**"""
+"""
+Includes objects and methods used for detection of particles by RodTracker.
+
+**Author:**     Adrian Niemann (adrian.niemann@ovgu.de)\n
+**Date:**       2022-2024
+"""
 
 import logging
 from pathlib import Path

diff --git a/RodTracker/src/RodTracker/backend/file_locations.py b/RodTracker/src/RodTracker/backend/file_locations.py
@@ -14,7 +14,13 @@
 # You should have received a copy of the GNU General Public License
 # along with RodTracker. If not, see <http://www.gnu.org/licenses/>.
 
-"""**TBD**"""
+"""
+Auxillary methods for getting paths to application icon/logo and opening
+documentation.
+
+**Author:**     Adrian Niemann (adrian.niemann@ovgu.de)\n
+**Date:**       2022-2024
+"""
 
 import logging
 import os

diff --git a/RodTracker/src/RodTracker/backend/img_data.py b/RodTracker/src/RodTracker/backend/img_data.py
@@ -14,13 +14,19 @@
 # You should have received a copy of the GNU General Public License
 # along with RodTracker. If not, see <http://www.gnu.org/licenses/>.
 
-"""**TBD**"""
+"""
+Class and methods called in RodTracked GUI application for loading and
+selection of images.
+
+**Author:**     Adrian Niemann (adrian.niemann@ovgu.de)\n
+**Date:**       2022-2024
+"""
 
 import logging
 from pathlib import Path
 from typing import List, Tuple
 
-from PyQt5 import QtCore, QtGui, QtWidgets
+from PyQt5 import QtCore, QtGui
 
 import RodTracker.backend.logger as lg
 import RodTracker.ui.dialogs as dialogs
@@ -124,25 +130,20 @@ def select_images(self, pre_selection: str = ""):
         if chosen_folder is None:
             # File selection was aborted
             return
-        # Find and hand over the first file in the chosen directory
-        for file in chosen_folder.iterdir():
-            if file.is_dir():
-                continue
-            self.open_image_folder(file)
-            return
+        self.open_image_folder(chosen_folder)
 
-    def open_image_folder(self, chosen_file: Path):
-        """Tries to open an image folder to show the given image.
+    def open_image_folder(self, chosen_folder: Path):
+        """Attempts to open an image folder and show the first image.
 
         All images of the folder from the chosen file's folder are marked for
-        later display. The selected image is opened immediately. It tries to
-        extract a camera id from the selected folder and logs the
-        opening action.
+        later display. The first image is opened immediately. It tries to
+        extract a camera id from the selected folder and logs the opening
+        action.
 
         Parameters
         ----------
-        chosen_file: Path
-            Path to image file chosen for immediate display.
+        chosen_folder: Path
+            Path to chosen folder.
 
         Returns
         -------
@@ -157,27 +158,34 @@ def open_image_folder(self, chosen_file: Path):
             - :attr:`next_img` [int, int]
             - :attr:`data_loaded`
         """
-        if not chosen_file:
+        if not chosen_folder:
+            return
+        chosen_folder = chosen_folder.resolve()
+        files, frames = get_images(chosen_folder)
+        if len(files) == 0:
+            _logger.warning(
+                "No valid frames found in the selected folder: "
+                f"{chosen_folder}"
+            )
+            dialogs.show_warning(
+                "No valid frames found in the selected folder:\n"
+                f"{chosen_folder}"
+            )
             return
-        chosen_file = chosen_file.resolve()
-        frame = int(chosen_file.stem.split("_")[-1])
+        # Sort according to name / ascending order
+        files.sort()
+        frames.sort()
+
         # Open file
-        loaded_image = QtGui.QImage(str(chosen_file))
+        loaded_image = QtGui.QImage(str(files[0]))
         if loaded_image.isNull():
-            QtWidgets.QMessageBox.information(
-                None, "Image Viewer", f"Cannot load {chosen_file}"
-            )
+            dialogs.show_warning(f"Cannot load {files[0]}")
             return
-        # Directory
-        self.folder = chosen_file.parent
-        self.files, self.frames = get_images(self.folder)
-        self.frame_idx = self.frames.index(frame)
 
-        # Sort according to name / ascending order
-        desired_file = self.files[self.frame_idx]
-        self.files.sort()
-        self.frame_idx = self.files.index(desired_file)
-        self.frames.sort()
+        self.folder = chosen_folder
+        self.files = files
+        self.frames = frames
+        self.frame_idx = 0
 
         # Get camera id for data display
         self.data_id = self.folder.name
@@ -303,9 +311,14 @@ def get_images(read_dir: Path) -> Tuple[List[Path], List[int]]:
     file_ids = []
     for f in read_dir.iterdir():
         if f.is_file() and f.suffix in [".png", ".jpg", ".jpeg"]:
-            # Add all image files to a list
+            try:
+                # Split any non-frame describing part of the filename and
+                # convert to integer (frame number)
+                tmp_id = int(f.stem.split("_")[-1])
+            except ValueError:
+                _logger.debug(f"Invalid file naming: {f}")
+                continue
+            # Add all image files and frame IDs to a output
+            file_ids.append(tmp_id)
             files.append(f)
-            # Split any non-frame describing part of the filename
-            tmp_id = f.stem.split("_")[-1]
-            file_ids.append(int(tmp_id))
     return files, file_ids
diff --git a/RodTracker/src/RodTracker/backend/logger.py b/RodTracker/src/RodTracker/backend/logger.py
@@ -14,7 +14,13 @@
 # You should have received a copy of the GNU General Public License
 # along with RodTracker. If not, see <http://www.gnu.org/licenses/>.
 
-"""**TBD**"""
+"""
+Class and methods used in RodTracked GUI for manipulation with particles
+coordinate data and logging the resulting actions.
+
+**Author:**     Adrian Niemann (adrian.niemann@ovgu.de)\n
+**Date:**       2022-2024
+"""
 
 import logging
 import pathlib

diff --git a/RodTracker/src/RodTracker/backend/parallelism.py b/RodTracker/src/RodTracker/backend/parallelism.py
@@ -14,7 +14,14 @@
 # You should have received a copy of the GNU General Public License
 # along with RodTracker. If not, see <http://www.gnu.org/licenses/>.
 
-"""**TBD**"""
+"""
+Classes used in RodTracked GUI for parallel thread work
+(some lengthy computations/data loading is performed outside
+of the main thread).
+
+**Author:**     Adrian Niemann (adrian.niemann@ovgu.de)\n
+**Date:**       2022-2024
+"""
 
 import sys
 from functools import wraps