pre release changes (#94)

* change from RGB2GRAY to RGB2BGR

* remove gray scale conv

* change get_frames_from_idxs

* remove diffrent markers for diffrent views

* add two steps zip and download project file

* fix empty video error in video player

* remove color for same bodyparts

* flaked

* fix tests

lightning_pose_app/backend/extract_frames.py

@@ -57,7 +57,7 @@ def read_nth_frames(
                 # If the frame was successfully read, then process it
                 if frame_counter % n == 0:
                     frame_resize = cv2.resize(frame, (resize_dims, resize_dims))
-                    frame_gray = cv2.cvtColor(frame_resize, cv2.COLOR_BGR2GRAY)
+                    frame_gray = cv2.cvtColor(frame_resize, cv2.COLOR_BGR2RGB)
                     frames.append(frame_gray.astype(np.float16))
                 frame_counter += 1
                 progress = frame_counter / frame_total * 100.0
@@ -344,7 +344,7 @@ def export_frames(
     for frame, idx in zip(frames, frame_idxs):
         cv2.imwrite(
             filename=os.path.join(save_dir, "img%s.%s" % (str(idx).zfill(n_digits), format)),
-            img=frame[0],
+            img=cv2.cvtColor(frame.transpose(1, 2, 0), cv2.COLOR_RGB2BGR),
         )
 
 
@@ -394,28 +394,28 @@ def convert_csv_to_dict(csv_path: str, selected_body_parts: list = None) -> dict
 
 def annotate_frames(image_path: str, annotations: dict, output_path: str):
     try:
-        image = Image.open(image_path).convert('L')
-        fig, ax = plt.subplots()
-
-        ax.imshow(image, cmap="gray")
+        image = Image.open(image_path)
+        # Convert image to RGB if necessary
+        if image.mode == 'L':
+            image = image.convert('L')
+        elif image.mode != 'RGB':
+            image = image.convert('RGB')
 
-        # Get a list of unique body parts and determine colors
-        unique_bodyparts = list(set([label.split('_')[0] for label in annotations.keys()]))
-        unique_views = list(set([label.split('_')[1] for label in annotations.keys()]))
+        fig, ax = plt.subplots()
+        ax.imshow(image, cmap='gray' if image.mode == 'L' else None)
+        # Get a list of unique body parts
+        unique_bodyparts = list(set(annotations.keys()))
 
         color_map = plt.cm.get_cmap('tab10', len(unique_bodyparts))
         bodypart_colors = {bodypart: color_map(i) for i, bodypart in enumerate(unique_bodyparts)}
 
-        # Create suffix_marker_map dynamically
         markers = ['o', '^', 's', 'p', '*', 'x', 'd', 'v', '<', '>']
-        suffix_marker_map = {
-            view: markers[i % len(markers)]
-            for i, view
-            in enumerate(unique_views)
+        bodypart_markers = {
+            bodypart: markers[i % len(markers)] for i, bodypart in enumerate(unique_bodyparts)
         }
 
         img_width, img_height = image.size
-        font_size = max(6, min(img_width, img_height) // 50)
+        font_size = max(6, min(img_width, img_height) // 100)
 
         for label, coords in annotations.items():
             try:
@@ -427,10 +427,9 @@ def annotate_frames(image_path: str, annotations: dict, output_path: str):
                     _logger.warning(f"Missing x or y in annotation for {label}")
                     continue
 
-                bodypart = label.split('_')[0]
-                view = label.split('_')[1]
+                bodypart = label
                 color = bodypart_colors[bodypart]
-                marker = suffix_marker_map[view]
+                marker = bodypart_markers[bodypart]
 
                 ax.plot(x, y, marker, color=color, markersize=3)
 
@@ -445,7 +444,8 @@ def annotate_frames(image_path: str, annotations: dict, output_path: str):
         frame_number = int(get_frame_number(image_path)[0])
 
         title_text = f'Video: {video} | Frame: {frame_number}'
-        ax.set_title(title_text, fontsize=font_size, pad=15)
+
+        ax.set_title(title_text, fontsize=10, pad=15)
         ax.axis('off')
 
         # Ensure the output directory exists

lightning_pose_app/backend/video.py

@@ -137,10 +137,11 @@ def get_frames_from_idxs(cap: cv2.VideoCapture, idxs: np.ndarray) -> np.ndarray:
             cap.set(1, i)
         ret, frame = cap.read()
         if ret:
+            frame_rgb = cv2.cvtColor(frame, cv2.COLOR_BGR2RGB)
             if fr == 0:
-                height, width, _ = frame.shape
-                frames = np.zeros((n_frames, 1, height, width), dtype="uint8")
-            frames[fr, 0, :, :] = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+                height, width, _ = frame_rgb.shape
+                frames = np.zeros((n_frames, 3, height, width), dtype="uint8")
+            frames[fr] = frame_rgb.transpose(2, 0, 1)
         else:
             _logger.debug(
                 "warning! reached end of video; returning blank frames for remainder of "

lightning_pose_app/ui/project.py

@@ -578,9 +578,10 @@ def _render_streamlit_fn(state: AppState):
                 sorted(state.initialized_projects)
             )
             st.markdown(
-                "Project exports only contain frames, labels, and the project config file."
-                "To download trained models or the results files from video inference, see [here]."
-                "(https://pose-app.readthedocs.io/en/latest/source/accessing_your_data.html#)",
+                "Project exports only contain frames, labels, and the project config file. "
+                "To download trained models or the results files from video inference, see "
+                "[here]"
+                "(https://pose-app.readthedocs.io/en/latest/source/accessing_your_data.html#).",
                 unsafe_allow_html=True,
             )
 
@@ -594,20 +595,26 @@ def _render_streamlit_fn(state: AppState):
                         "Please label some frames before attempting to download the project."
                     )
                 else:
-                    try:
-                        zip_filepath = zip_project_for_export(proj_dir)
-                        # Add download botton
-                        with open(zip_filepath, "rb") as f:
+                    if 'zip_filepath' not in st.session_state:
+                        st.session_state.zip_filepath = None
+                    if st.button("Zip Project Files"):
+                        try:
+                            st.session_state.zip_filepath = zip_project_for_export(proj_dir)
+                            st.success(
+                                "Project files are zipped and ready. Press the button below to "
+                                "download the zipped files."
+                            )
+                        except FileNotFoundError as e:
+                            st.error(str(e))
+                    if st.session_state.zip_filepath:
+                        with open(st.session_state.zip_filepath, "rb") as f:
                             st.download_button(
                                 label="Download Project",
                                 data=f,
-                                file_name=os.path.basename(zip_filepath)
+                                file_name=os.path.basename(st.session_state.zip_filepath)
                             )
-                        os.remove(zip_filepath)
-
-                    except FileNotFoundError as e:
-                        st.error(str(e))
-
+                        os.remove(st.session_state.zip_filepath)
+                        st.session_state.zip_filepath = None
     st.header("Manage Lightning Pose projects")
 
     st_mode = st.radio(

lightning_pose_app/ui/streamlit_video_viewer.py

@@ -82,46 +82,51 @@ def _render_streamlit_fn(state: AppState):
             )
             st.divider()
             # Add a section to download results files
-            video_name = extract_video_name(selected_video)
-            results_files = list_results_files(video_name, model_dir, selected_model)
-
-            if results_files:
-                selected_result_files = st.multiselect(
-                    "**Step 3:** Select results files to download", list(results_files.keys())
-                )
-                if selected_result_files:
-                    if len(selected_result_files) == 1:
-                        selected_result_file = results_files[selected_result_files[0]]
-                        new_file_name = f"{selected_model}_{video_name}_{selected_result_files[0]}"
-                        with open(selected_result_file, "rb") as file:
+            if selected_video:
+                video_name = extract_video_name(selected_video)
+                results_files = list_results_files(video_name, model_dir, selected_model)
+
+                if results_files:
+                    selected_result_files = st.multiselect(
+                        "**Step 3:** Select results files to download", list(results_files.keys())
+                    )
+                    if selected_result_files:
+                        if len(selected_result_files) == 1:
+                            selected_result_file = results_files[selected_result_files[0]]
+                            new_file_name = (
+                                f"{selected_model}_{video_name}_{selected_result_files[0]}"
+                            )
+                            with open(selected_result_file, "rb") as file:
+                                st.download_button(
+                                    label="Download File",
+                                    data=file,
+                                    file_name=new_file_name
+                                )
+                        else:
+                            st.warning(
+                                "If you select more than one file, they will be downloaded "
+                                "together as a ZIP folder"
+                            )
+                            # Create a zip file
+                            zip_buffer = BytesIO()
+                            with zipfile.ZipFile(zip_buffer, "w") as zip_file:
+                                for result_file_name in selected_result_files:
+                                    result_file_path = results_files[result_file_name]
+                                    new_file_name = (
+                                        f"{selected_model}_{video_name}_{result_file_name}"
+                                    )
+                                    with open(result_file_path, "rb") as file:
+                                        zip_file.writestr(new_file_name, file.read())
+                            zip_buffer.seek(0)
+                            zip_file_name = f"results_{selected_model}_{video_name}.zip"
                             st.download_button(
-                                label="Download File",
-                                data=file,
-                                file_name=new_file_name
+                                label="Download Files",
+                                data=zip_buffer,
+                                file_name=zip_file_name,
+                                mime="application/zip"
                             )
-                    else:
-                        st.warning(
-                            "If you select more than one file, they will be downloaded "
-                            "together as a ZIP folder"
-                        )
-                        # Create a zip file
-                        zip_buffer = BytesIO()
-                        with zipfile.ZipFile(zip_buffer, "w") as zip_file:
-                            for result_file_name in selected_result_files:
-                                result_file_path = results_files[result_file_name]
-                                new_file_name = f"{selected_model}_{video_name}_{result_file_name}"
-                                with open(result_file_path, "rb") as file:
-                                    zip_file.writestr(new_file_name, file.read())
-                        zip_buffer.seek(0)
-                        zip_file_name = f"results_{selected_model}_{video_name}.zip"
-                        st.download_button(
-                            label="Download Files",
-                            data=zip_buffer,
-                            file_name=zip_file_name,
-                            mime="application/zip"
-                        )
-            else:
-                st.write("No results files available for this video.")
+                else:
+                    st.write("No results files available for this video.")
 
         if selected_video:
             # read and show the predictions labeled video

tests/backend/test_backend_extract_frames.py

@@ -15,7 +15,7 @@ def test_read_nth_frames(video_file):
 
     resize_dims = 8
     frames = read_nth_frames(video_file=video_file, n=10, resize_dims=resize_dims)
-    assert frames.shape == (100, resize_dims, resize_dims)
+    assert frames.shape == (100, resize_dims, resize_dims, 3)
 
 
 def test_select_idxs_kmeans(video_file):

tests/backend/test_backend_video.py

@@ -50,7 +50,7 @@ def test_get_frames_from_idxs(video_file):
     n_frames = 3
     frames = get_frames_from_idxs(cap, np.arange(n_frames))
     cap.release()
-    assert frames.shape == (n_frames, 1, 406, 396)
+    assert frames.shape == (n_frames, 3, 406, 396)
     assert frames.dtype == np.uint8