video tools

simba/SimBA.py

@@ -131,7 +131,7 @@
     ImportFrameDirectoryPopUp, InitiateClipMultipleVideosByFrameNumbersPopUp,
     InitiateClipMultipleVideosByTimestampsPopUp, MergeFrames2VideoPopUp,
     MultiCropPopUp, MultiShortenPopUp, SuperImposeFrameCountPopUp,
-    VideoRotatorPopUp, VideoTemporalJoinPopUp)
+    VideoRotatorPopUp, VideoTemporalJoinPopUp, BrightnessContrastPopUp, InteractiveClahePopUp)
 from simba.ui.pop_ups.visualize_pose_in_dir_pop_up import \
     VisualizePoseInFolderPopUp
 from simba.ui.tkinter_functions import DropDownMenu, Entry_Box, FileSelect
@@ -1678,31 +1678,16 @@ def __init__(self):
         )
 
         format_menu = Menu(video_process_menu)
-        format_menu.add_command(
-            label="Change image file formats", command=ChangeImageFormatPopUp
-        )
-        format_menu.add_command(
-            label="Change video file formats", command=ConvertVideoPopUp
-        )
-        video_process_menu.add_cascade(
-            label="Change formats...",
-            compound="left",
-            image=self.menu_icons["convert"]["img"],
-            menu=format_menu,
-        )
-        video_process_menu.add_command(
-            label="CLAHE enhance video",
-            compound="left",
-            image=self.menu_icons["clahe"]["img"],
-            command=CLAHEPopUp,
-        )
+        format_menu.add_command(label="Change image file formats", command=ChangeImageFormatPopUp)
+        format_menu.add_command(label="Change video file formats", command=ConvertVideoPopUp)
+        video_process_menu.add_cascade(label="Change formats...", compound="left", image=self.menu_icons["convert"]["img"], menu=format_menu)
 
-        video_process_menu.add_cascade(
-            label="Concatenate multiple videos",
-            compound="left",
-            image=self.menu_icons["concat"]["img"],
-            command=lambda: ConcatenatorPopUp(config_path=None),
-        )
+        clahe_menu = Menu(video_process_menu)
+        clahe_menu.add_command(label="CLAHE enhance videos", command=CLAHEPopUp)
+        clahe_menu.add_command(label="Interactively CLAHE enhance videos", command=InteractiveClahePopUp)
+        video_process_menu.add_cascade(label="CLAHE enhance videos...", compound="left", image=self.menu_icons["clahe"]["img"], menu=clahe_menu)
+
+        video_process_menu.add_cascade(label="Concatenate multiple videos", compound="left", image=self.menu_icons["concat"]["img"], command=lambda: ConcatenatorPopUp(config_path=None))
         video_process_menu.add_cascade(
             label="Concatenate two videos",
             compound="left",
@@ -1722,12 +1707,9 @@ def __init__(self):
             command=lambda: ConvertROIDefinitionsPopUp(),
         )
         convert_data_menu = Menu(video_process_menu)
-        convert_data_menu.add_command(
-            label="Convert CSV to parquet", command=Csv2ParquetPopUp
-        )
-        convert_data_menu.add_command(
-            label="Convert parquet o CSV", command=Parquet2CsvPopUp
-        )
+        convert_data_menu.add_command(label="Convert CSV to parquet", command=Csv2ParquetPopUp)
+        convert_data_menu.add_command(label="Convert parquet o CSV", command=Parquet2CsvPopUp)
+
         video_process_menu.add_cascade(
             label="Convert working file type...",
             compound="left",
@@ -1784,6 +1766,10 @@ def __init__(self):
             image=self.menu_icons["calipher"]["img"],
             command=CalculatePixelsPerMMInVideoPopUp,
         )
+
+        video_process_menu.add_command(label="Change video brightness / contrast", compound="left", image=self.menu_icons["brightness"]["img"], command=BrightnessContrastPopUp)
+
+
         video_process_menu.add_command(
             label="Merge frames to video",
             compound="left",

simba/mixins/statistics_mixin.py

@@ -3186,6 +3186,41 @@ def manhattan_distance_cdist(data: np.ndarray) -> np.ndarray:
         results = np.sum(differences, axis=-1)
         return results
 
+    @staticmethod
+    @jit('(float32[:,:],)')
+    def mahalanobis_distance_cdist(data: np.ndarray) -> np.ndarray:
+        """
+        Compute the Mahalanobis distance between every pair of observations in a 2D array using numba.
+
+        The Mahalanobis distance is a measure of the distance between a point and a distribution. It accounts for correlations between variables and the scales of the variables, making it suitable for datasets where features are not independent and have different variances.
+
+        .. note::
+           Significantly reduced runtime versus Mahalanobis scipy.cdist only with larger feature sets ( > 10-50).
+
+        However, Mahalanobis distance may not be suitable in certain scenarios, such as:
+        - When the dataset is small and the covariance matrix is not accurately estimated.
+        - When the dataset contains outliers that significantly affect the estimation of the covariance matrix.
+        - When the assumptions of multivariate normality are violated.
+
+        :param np.ndarray data: 2D array with feature observations. Frames on axis 0 and feature values on axis 1
+        :return np.ndarray: Pairwise Mahalanobis distance matrix where element (i, j) represents the Mahalanobis distance between  observations i and j.
+
+        :example:
+        >>> data = np.random.randint(0, 50, (1000, 200)).astype(np.float32)
+        >>> x = mahalanobis_distance_cdist(data=data)
+        """
+
+        covariance_matrix = np.cov(data, rowvar=False)
+        inv_covariance_matrix = np.linalg.inv(covariance_matrix).astype(np.float32)
+        n = data.shape[0]
+        distances = np.zeros((n, n))
+        for i in prange(n):
+            for j in range(n):
+                diff = data[i] - data[j]
+                diff = diff.astype(np.float32)
+                distances[i, j] = np.sqrt(np.dot(np.dot(diff, inv_covariance_matrix), diff.T))
+        return distances
+
     @staticmethod
     @njit("(int64[:], int64[:])")
     def cohens_kappa(sample_1: np.ndarray, sample_2: np.ndarray):

simba/ui/pop_ups/video_processing_pop_up.py

@@ -6,6 +6,8 @@
 import threading
 from tkinter import *
 from typing import Optional, Union
+import subprocess
+from datetime import datetime
 
 from PIL import Image, ImageTk
 
@@ -14,6 +16,8 @@
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.pop_up_mixin import PopUpMixin
 from simba.plotting.frame_mergerer_ffmpeg import FrameMergererFFmpeg
+from simba.video_processors.brightness_contrast_ui import brightness_contrast_ui
+from simba.video_processors.clahe_ui import interactive_clahe_ui
 from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon,
                                         CreateToolTip, DropDownMenu, Entry_Box,
                                         FileSelect, FolderSelect)
@@ -32,7 +36,7 @@
 from simba.utils.read_write import (
     check_if_hhmmss_timestamp_is_valid_part_of_video,
     concatenate_videos_in_folder, find_all_videos_in_directory, get_fn_ext,
-    get_video_meta_data, seconds_to_timestamp)
+    get_video_meta_data, seconds_to_timestamp, find_files_of_filetypes_in_directory)
 from simba.video_processors.extract_seqframes import extract_seq_frames
 from simba.video_processors.multi_cropper import MultiCropper
 from simba.video_processors.px_to_mm import get_coordinates_nilsson
@@ -55,33 +59,47 @@
 class CLAHEPopUp(PopUpMixin):
     def __init__(self):
         super().__init__(title="CLAHE VIDEO CONVERSION")
-        clahe_frm = CreateLabelFrameWithIcon(
-            parent=self.main_frm,
-            header="Contrast Limited Adaptive Histogram Equalization",
-            icon_name=Keys.DOCUMENTATION.value,
-            icon_link=Links.VIDEO_TOOLS.value,
-        )
-        selected_video = FileSelect(
-            clahe_frm,
-            "Video path ",
-            title="Select a video file",
-            file_types=[("VIDEO", Options.ALL_VIDEO_FORMAT_STR_OPTIONS.value)],
-        )
-        button_clahe = Button(
-            clahe_frm,
-            text="Apply CLAHE",
-            command=lambda: threading.Thread(
-                target=clahe_enhance_video(file_path=selected_video.file_path)
-            ).start(),
-        )
+        single_video_frm = CreateLabelFrameWithIcon(parent=self.main_frm,
+                                                    header="SINGLE VIDEO - Contrast Limited Adaptive Histogram Equalization",
+                                                    icon_name=Keys.DOCUMENTATION.value,
+                                                    icon_link=Links.VIDEO_TOOLS.value)
+        self.selected_video = FileSelect(single_video_frm, "VIDEO PATH:", title="Select a video file", file_types=[("VIDEO", Options.ALL_VIDEO_FORMAT_STR_OPTIONS.value)], lblwidth=25)
+        run_single_video_btn = Button(single_video_frm, text="Apply CLAHE on VIDEO", command=lambda: self.run_single_video(),  fg="blue")
+
+        multiple_videos_frm = CreateLabelFrameWithIcon(parent=self.main_frm,
+                                                       header="MULTIPLE VIDEOs - Contrast Limited Adaptive Histogram Equalization",
+                                                       icon_name=Keys.DOCUMENTATION.value,
+                                                       icon_link=Links.VIDEO_TOOLS.value)
+        self.selected_dir = FolderSelect(multiple_videos_frm, "VIDEO DIRECTORY PATH:", lblwidth=25)
+        run_multiple_btn = Button(multiple_videos_frm, text="Apply CLAHE on DIRECTORY", command=lambda: self.run_directory(), fg="blue")
+
+        single_video_frm.grid(row=0, column=0, sticky=NW)
+        self.selected_video.grid(row=0, column=0, sticky=NW)
+        run_single_video_btn.grid(row=1, column=0, sticky=NW)
 
-        clahe_frm.grid(row=0, sticky=W)
-        selected_video.grid(row=0, sticky=W)
-        button_clahe.grid(row=1, pady=5)
-        # self.main_frm.mainloop()
+        multiple_videos_frm.grid(row=1, column=0, sticky=NW)
+        self.selected_dir.grid(row=0, column=0, sticky=NW)
+        run_multiple_btn.grid(row=1, column=0, sticky=NW)
+        #self.main_frm.mainloop()
 
 
-# _ = CLAHEPopUp()
+    def run_single_video(self):
+        selected_video = self.selected_video.file_path
+        check_file_exist_and_readable(file_path=selected_video)
+        threading.Thread(target=clahe_enhance_video(file_path=selected_video)).start()
+
+    def run_directory(self):
+        timer = SimbaTimer(start=True)
+        video_dir = self.selected_dir.folder_path
+        check_if_dir_exists(in_dir=video_dir, source=self.__class__.__name__)
+        self.video_paths = find_files_of_filetypes_in_directory(directory=video_dir, extensions=Options.ALL_VIDEO_FORMAT_OPTIONS.value, raise_error=True)
+        for file_path in self.video_paths:
+            threading.Thread(target=clahe_enhance_video(file_path=file_path)).start()
+        timer.stop_timer()
+        stdout_success(msg=f'CLAHE enhanced {len(self.video_paths)} video(s)', elapsed_time=timer.elapsed_time_str)
+
+
+#_ = CLAHEPopUp()
 
 
 class CropVideoPopUp(PopUpMixin):
@@ -2047,6 +2065,110 @@ def run(self):
             save_dir=self.output_folder.folder_path,
         )
 
+class BrightnessContrastPopUp(PopUpMixin):
+    def __init__(self):
+        super().__init__(title="CHANGE BRIGHTNESS / CONTRAST")
+        self.datetime = datetime.now().strftime("%Y%m%d%H%M%S")
+        single_video_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="CHANGE BRIGHTNESS / CONTRAST SINGLE VIDEO", icon_name=Keys.DOCUMENTATION.value, icon_link=Links.VIDEO_TOOLS.value)
+        self.selected_video = FileSelect(single_video_frm, "VIDEO PATH:", title="Select a video file", file_types=[("VIDEO", Options.ALL_VIDEO_FORMAT_STR_OPTIONS.value)], lblwidth=25)
+        run_video_btn = Button(single_video_frm, text="RUN SINGLE VIDEO", command=lambda: self.run_video(), fg="blue")
+
+        single_video_frm.grid(row=0, column=0, sticky="NW")
+        self.selected_video.grid(row=0, column=0, sticky="NW")
+        run_video_btn.grid(row=1, column=0, sticky="NW")
+
+        video_dir_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="CHANGE BRIGHTNESS / CONTRAST MULTIPLE VIDEOS", icon_name=Keys.DOCUMENTATION.value, icon_link=Links.VIDEO_TOOLS.value)
+        self.selected_dir = FolderSelect(video_dir_frm, "VIDEO DIRECTORY PATH:", lblwidth=25)
+        run_dir_btn = Button(video_dir_frm, text="RUN VIDEO DIRECTORY", command=lambda: self.run_directory(), fg="blue")
+
+        video_dir_frm.grid(row=1, column=0, sticky="NW")
+        self.selected_dir.grid(row=0, column=0, sticky="NW")
+        run_dir_btn.grid(row=1, column=0, sticky="NW")
+        self.main_frm.mainloop()
+
+    def run_video(self):
+        video_path = self.selected_video.file_path
+        check_file_exist_and_readable(file_path=video_path)
+        self.brightness, self.contrast = brightness_contrast_ui(video_path=video_path)
+        self.video_paths = [video_path]
+        self.apply()
+
+    def run_directory(self):
+        video_dir = self.selected_dir.folder_path
+        check_if_dir_exists(in_dir=video_dir, source=self.__class__.__name__)
+        self.video_paths = find_files_of_filetypes_in_directory(directory=video_dir, extensions=Options.ALL_VIDEO_FORMAT_OPTIONS.value, raise_error=True)
+        self.brightness, self.contrast = brightness_contrast_ui(video_path=self.video_paths[0])
+        self.apply()
+
+    def apply(self):
+        timer = SimbaTimer(start=True)
+        for file_cnt, file_path in enumerate(self.video_paths):
+            video_timer = SimbaTimer(start=True)
+            dir, video_name, ext = get_fn_ext(filepath=file_path)
+            print(f'Creating copy of {video_name}...')
+            out_path = os.path.join(dir, f'{video_name}_eq_{self.datetime}{ext}')
+            cmd = f'ffmpeg -i "{file_path}" -vf "eq=brightness={self.brightness}:contrast={self.contrast}" -loglevel error -stats "{out_path}" -y'
+            subprocess.call(cmd, shell=True, stdout=subprocess.PIPE)
+            video_timer.stop_timer()
+            stdout_success(msg=f'Video {out_path} complete!', elapsed_time=video_timer.elapsed_time_str)
+        timer.stop_timer()
+        stdout_success(f'{len(self.video_paths)} video(s) converted.', elapsed_time=timer.elapsed_time_str)
+
+
+class InteractiveClahePopUp(PopUpMixin):
+    """
+    .. image:: _static/img/interactive_clahe_ui.gif
+       :width: 500
+       :align: center
+    """
+
+    def __init__(self):
+        super().__init__(title="INTERACTIVE CLAHE")
+        self.datetime = datetime.now().strftime("%Y%m%d%H%M%S")
+        single_video_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="INTERACTIVE CLAHE - SINGLE VIDEO", icon_name=Keys.DOCUMENTATION.value, icon_link=Links.VIDEO_TOOLS.value)
+        self.selected_video = FileSelect(single_video_frm, "VIDEO PATH:", title="Select a video file", file_types=[("VIDEO", Options.ALL_VIDEO_FORMAT_STR_OPTIONS.value)], lblwidth=25)
+        run_video_btn = Button(single_video_frm, text="RUN SINGLE VIDEO", command=lambda: self.run_video(), fg="blue")
+
+        single_video_frm.grid(row=0, column=0, sticky="NW")
+        self.selected_video.grid(row=0, column=0, sticky="NW")
+        run_video_btn.grid(row=1, column=0, sticky="NW")
+
+        video_dir_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="INTERACTIVE CLAHE - MULTIPLE VIDEOS", icon_name=Keys.DOCUMENTATION.value, icon_link=Links.VIDEO_TOOLS.value)
+        self.selected_dir = FolderSelect(video_dir_frm, "VIDEO DIRECTORY PATH:", lblwidth=25)
+        run_dir_btn = Button(video_dir_frm, text="RUN VIDEO DIRECTORY", command=lambda: self.run_directory(), fg="blue")
+
+        video_dir_frm.grid(row=1, column=0, sticky="NW")
+        self.selected_dir.grid(row=0, column=0, sticky="NW")
+        run_dir_btn.grid(row=1, column=0, sticky="NW")
+        self.main_frm.mainloop()
+
+    def run_video(self):
+        video_path = self.selected_video.file_path
+        check_file_exist_and_readable(file_path=video_path)
+        self.clip_limit, self.tile_size = interactive_clahe_ui(data=video_path)
+        self.video_paths = [video_path]
+        self.apply()
+
+    def run_directory(self):
+        video_dir = self.selected_dir.folder_path
+        check_if_dir_exists(in_dir=video_dir, source=self.__class__.__name__)
+        self.video_paths = find_files_of_filetypes_in_directory(directory=video_dir, extensions=Options.ALL_VIDEO_FORMAT_OPTIONS.value, raise_error=True)
+        self.clip_limit, self.tile_size = interactive_clahe_ui(data=self.video_paths[0])
+        self.apply()
+
+    def apply(self):
+        timer = SimbaTimer(start=True)
+        for file_cnt, file_path in enumerate(self.video_paths):
+            dir, video_name, ext = get_fn_ext(filepath=file_path)
+            print(f'Creating CLAHE copy of {video_name}...')
+            out_path = os.path.join(dir, f'{video_name}_CLAHE_CLIPLIMIT_{int(self.clip_limit)}_TILESIZE_{int(self.tile_size)}_{self.datetime}{ext}')
+            clahe_enhance_video(file_path=file_path, clip_limit=int(self.clip_limit), tile_grid_size=(int(self.tile_size), int(self.tile_size)), out_path=out_path)
+        timer.stop_timer()
+        stdout_success(f'{len(self.video_paths)} video(s) converted.', elapsed_time=timer.elapsed_time_str)
+
+
+
+
 
 # ClipMultipleVideosByFrameNumbers
 # ClipMultipleVideosByFrameNumbers(data_dir='/Users/simon/Desktop/envs/simba/troubleshooting/beepboop174/project_folder/videos/test', save_dir='/Users/simon/Desktop/envs/simba/troubleshooting/beepboop174/project_folder/videos/clipped')