Add notebook to explore trajectories of escape clips (#257)

* add movement as dependency

* Rename existing movement notebook

* Add notebooks dependencies

* Rename old movement notebook

* Add notebook to generate plot of escape clips

* Update path

* Add plot saving

* Add as a script (to run in interactive job in the cluster)

* Small edits to script

* Update notebook

* Add notebook for visualising trajectories with movement

* Add last version of .py vscode notebook (to keep it in history)

* Delete duplicate

* Remove movement as dependency and `[notebooks]` as an extra

MANIFEST.in

@@ -6,6 +6,7 @@ recursive-include guides *.md
 recursive-include crabs/tracker *.md
 recursive-include bash_scripts *.sh
 recursive-include notebooks *.py
+recursive-include notebooks *.ipynb
 recursive-include scripts *.py
 recursive-include crabs *.yaml
 recursive-include guides *.png

notebooks/notebook_trajectories_movement.py → notebooks/notebook_movement_trajectories_gt.py

@@ -1,4 +1,4 @@
-"""Inspect crab trajectories using movement"""
+"""Inspect crab groundtruth clip using movement"""
 
 # %%
 import itertools
@@ -22,8 +22,8 @@
 
 # load ground truth (corrected)
 groundtruth_csv_corrected = (
-    "/Users/sofia/arc/project_Zoo_crabs/escape_clips/"
-    "04.09.2023-04-Right_RE_test_corrected_ST_csv_SM_corrected.csv"
+    "/Users/sofia/arc/project_Zoo_crabs/tracking_groundtruth_generation/"
+    "04.09.2023-04-Right_RE_test_corrected_ST_SM_20241029_113207.csv"
 )
 
 

scripts/escape_trajectory_plots.py

@@ -0,0 +1,138 @@
+"""Generate trajectory plots for escape clips."""
+
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+from movement.io import load_bboxes
+
+
+def main(input_data, output_figures_dir):
+    """Read input files as movement datasets and generate plots."""
+    # Create a directory if it doesnt exist
+    if not output_figures_dir.exists():
+        output_figures_dir.mkdir(parents=True)
+
+    # List all csv files in the input directory
+    list_csv_files = [
+        x
+        for x in input_data.iterdir()
+        if x.is_file() and x.name.endswith("_tracks.csv")
+    ]
+    list_csv_files.sort()
+    print(len(list_csv_files))
+
+    # Prepare plots
+    # select whether to plot ID at first frame
+    flag_plot_id = False
+
+    # Define colors - ideally more than max n individuals
+    # so that we don't have repetitions
+    list_colors = (
+        plt.get_cmap("Pastel1").colors  # 9 colors
+        + plt.get_cmap("Pastel2").colors  # 8 colors
+        + plt.get_cmap("Paired").colors  # 12 colors
+        + plt.get_cmap("Accent").colors  # 8 colors
+        + plt.get_cmap("Dark2").colors  # 8 colors
+        + plt.get_cmap("Set1").colors  # 9 colors
+        + plt.get_cmap("Set3").colors  # 12 colors
+        + plt.get_cmap("tab20b").colors  # 10 colors
+        + plt.get_cmap("tab20c").colors  # 20 colors
+    )  # 96 colors
+
+    # loop thru escape clip files
+    for csv_file in list_csv_files:
+        # Create movement ds
+        ds = load_bboxes.from_via_tracks_file(
+            csv_file, fps=None, use_frame_numbers_from_file=False
+        )
+
+        # Print summary metrics
+        print(Path(ds.source_file).name)
+        print(f"Number of frames: {ds.sizes['time']}")
+        print(f"Number of individuals: {ds.sizes['individuals']}")
+        print(ds)
+        print("--------------------")
+
+        # Compute number of frames with non-nan position per ID
+        non_nan_frames_per_ID = {}
+        for ind, _id_str in enumerate(ds.individuals):
+            non_nan_frames_per_ID[ind] = (
+                len(ds.time)
+                - ds.position[:, ind, :].isnull().any(axis=1).sum().item()
+            )
+
+        # Plot trajectories per individual
+        fig, ax = plt.subplots(1, 1)
+        for ind_idx in range(ds.sizes["individuals"]):
+            # plot trajectories
+            ax.scatter(
+                x=ds.position[:, ind_idx, 0],  # nframes, nindividuals, x
+                y=ds.position[:, ind_idx, 1],
+                s=1,
+                color=list_colors[ind_idx % len(list_colors)],
+            )
+            # add ID at first frame with non-nan x-coord
+            if flag_plot_id:
+                start_frame = ds.time[~ds.position.isnull()[:, ind_idx, 0]][
+                    0
+                ].item()
+                ax.text(
+                    x=ds.position[start_frame, ind_idx, 0],
+                    y=ds.position[start_frame, ind_idx, 1],
+                    s=ds.individuals[ind_idx].item().split("_")[1],
+                    fontsize=8,
+                    color=list_colors[ind_idx % len(list_colors)],
+                )
+
+        ax.set_aspect("equal")
+        ax.set_xlim(-150, 4200)  # frame size: 4096x2160
+        ax.set_ylim(-150, 2250)  # frame size: 4096x2160
+        ax.set_xlabel("x (pixels)")
+        ax.set_ylabel("y (pixels)")
+        ax.set_title(Path(ds.source_file).stem)
+        ax.invert_yaxis()
+
+        # Save plot as png
+        plt.savefig(
+            output_figures_dir / f"{Path(ds.source_file).stem}_tracks.png",
+            dpi=300,
+            bbox_inches="tight",
+        )
+
+        # Plot histogram of trajectories' lengths
+        fig, ax = plt.subplots(1, 1)
+        ax.hist(
+            non_nan_frames_per_ID.values(),
+            bins=np.arange(0, len(ds.time) + 50, 50),
+            alpha=0.5,
+            label="Prediction",
+        )
+        ax.set_xlabel("n frames with same ID")
+        ax.set_ylabel("n trajectories")
+        ax.hlines(
+            y=len(ds.individuals),
+            xmin=0,
+            xmax=len(ds.time),
+            color="red",
+            label="n individuals",
+        )
+        ax.legend()
+        ax.set_title(Path(ds.source_file).stem)
+
+        # Save plot as png
+        plt.savefig(
+            output_figures_dir / f"{Path(ds.source_file).stem}_histogram.png",
+            dpi=300,
+            bbox_inches="tight",
+        )
+
+
+if __name__ == "__main__":
+    input_data = Path(
+        "/home/sminano/swc/project_crabs/escape_clips_tracking_output_slurm_5699097"
+    )
+
+    output_figures_dir = input_data / "figures"
+
+    main(input_data, output_figures_dir)