Yang-Sun with adding video and dlc! #15

yangsunhwang · 2024-12-17T20:20:58Z

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src/jdb_to_nwb/convert_video.py

calderast

Some minor changes - mostly renaming things to use snake case (lowercase separated by underscores) for stylistic consistency. I think we can probably remove adjustment of video timestamps and just do that in the alignment code after this.

TBH after doing a bunch of suggested changes the file got hard to read and then I didn't run it to test it bc I had already made the changes. Maybe accept the changes you think are good and we will do another review pass so it is less confusing with little suggestions everywhere

calderast · 2025-01-07T22:40:34Z

src/jdb_to_nwb/convert_video.py

+    # Convert arduino timestamps to corresponding photosmetry sample number
+    video_timestamps = adjust_video_timestamps(video_timestamps, photometry_start_in_arduino_time)


Suggested change

# Convert arduino timestamps to corresponding photosmetry sample number

video_timestamps = adjust_video_timestamps(video_timestamps, photometry_start_in_arduino_time)

# Adjust all arduino timestamps so the photometry starts at time zero

video_timestamps = np.subtract(video_timestamps, photometry_start_in_arduino_time)

we can remove the adjust_video_timestamps function and do the subtraction directly because it's just one line

now that I reread this code I don't think we even need to do this adjustment here - we use camera FPS for velocity/acceleration etc and all we do with video timestamps is return them, so we can do this adjustment later in the combined alignment code. IMO we should just return raw video timestamps?

calderast · 2025-01-07T22:42:53Z

src/jdb_to_nwb/convert_video.py

+def adjust_video_timestamps(video_timestamps: list, photometry_start_in_arduino_time: float):
+    """Convert video timestamps to corresponding sample number."""
+    # Adjust all arduino timestamps so the photometry starts at time zero
+    video_timestamps = np.subtract(video_timestamps, photometry_start_in_arduino_time)
+
+    return video_timestamps
+


Suggested change

def adjust_video_timestamps(video_timestamps: list, photometry_start_in_arduino_time: float):

"""Convert video timestamps to corresponding sample number."""

# Adjust all arduino timestamps so the photometry starts at time zero

video_timestamps = np.subtract(video_timestamps, photometry_start_in_arduino_time)

return video_timestamps

we can remove this bc we replaced it with the single line above

calderast · 2025-01-07T22:57:59Z

src/jdb_to_nwb/convert_video.py

+    # Get pixelsPerCm based on the date of the data collected
+    pixelsPerCm = assign_pixels_per_cm(metadata["date"])


Add option to assign pixels_per_cm in metadata for flexibility in case the maze was moved that day or something. Also make it all uppercase to match convention for constants

Suggested change

# Get pixelsPerCm based on the date of the data collected

pixelsPerCm = assign_pixels_per_cm(metadata["date"])

# If pixels_per_cm exists in metadata, use that value

if "pixels_per_cm" in metadata["video"]:

PIXELS_PER_CM = metadata["video"]["pixels_per_cm"]

# Otherwise, assign it based on the date of the experiment

else:

PIXELS_PER_CM = assign_pixels_per_cm(metadata["date"])

calderast · 2025-01-07T22:58:47Z

src/jdb_to_nwb/convert_video.py

+    video_timestamps = adjust_video_timestamps(video_timestamps, photometry_start_in_arduino_time)
+
+    # Read x and y position data and calculate velocity and acceleration
+    x, y, velocity, acceleration = read_dlc(deeplabcut_file_path, phot_dlc = phot_dlc, cutoff = 0.9, cam_fps = 15, pixelsPerCm)


Suggested change

x, y, velocity, acceleration = read_dlc(deeplabcut_file_path, phot_dlc = phot_dlc, cutoff = 0.9, cam_fps = 15, pixelsPerCm)

x, y, velocity, acceleration = read_dlc(deeplabcut_file_path, phot_dlc = phot_dlc, cutoff = 0.9, cam_fps = 15, pixels_per_cm = PIXELS_PER_CM)

calderast · 2025-01-07T23:03:04Z

src/jdb_to_nwb/convert_video.py

+    Assigns pixelsPerCm based on the provided date string in mmddyyyy format.
+    - date_str (str): Date string in 'mmddyyyy' format, e.g., '11122022'.
+
+    3.14 if video is before IM-1594(before 01012023). 2.3 before (01112024). 2.688 after (old maze)
+
+    Returns:
+    - float: The corresponding pixelsPerCm value.


make PIXELS_PER_CM uppercase in function documentation

Suggested change

Assigns pixelsPerCm based on the provided date string in mmddyyyy format.

- date_str (str): Date string in 'mmddyyyy' format, e.g., '11122022'.

3.14 if video is before IM-1594(before 01012023). 2.3 before (01112024). 2.688 after (old maze)

Returns:

- float: The corresponding pixelsPerCm value.

Assigns constant PIXELS_PER_CM based on the provided date string in MMDDYYYY format.

PIXELS_PER_CM is 3.14 if video is before IM-1594 (before 01012023), 2.3 before (01112024), or 2.688 after (old maze)

Args:

- date_str (str): Date string in MMDDYYYY format, e.g., '11122022'.

Returns:

- float: The corresponding PIXELS_PER_CM value.

calderast · 2025-01-07T23:04:45Z

src/jdb_to_nwb/convert_video.py

+    Position data is under the column names: cap_back and cap_front.
+    Cap_bak is the back of the rat implant (red), and cap_front is the front of the rat implant (green)
+
+    After reading the position data, the position data is used to calculate velocity and acceleration based on the camera fps and pixelsPerCm


Suggested change

After reading the position data, the position data is used to calculate velocity and acceleration based on the camera fps and pixelsPerCm

After reading the position data, the position data is used to calculate velocity and acceleration based on the camera fps and pixels_per_cm

calderast · 2025-01-07T23:05:39Z

src/jdb_to_nwb/convert_video.py

+    pixelJumpCutoff = 30 * pixelsPerCm
+    position.loc[position.x.notnull(),['x','y']] = detect_and_replace_jumps(
+        position.loc[position.x.notnull(),['x','y']].values,pixelJumpCutoff)


Suggested change

pixelJumpCutoff = 30 * pixelsPerCm

position.loc[position.x.notnull(),['x','y']] = detect_and_replace_jumps(

position.loc[position.x.notnull(),['x','y']].values,pixelJumpCutoff)

pixel_jump_cutoff = 30 * pixels_per_cm

position.loc[position.x.notnull(),['x','y']] = detect_and_replace_jumps(

position.loc[position.x.notnull(),['x','y']].values,pixel_jump_cutoff)

calderast · 2025-01-07T23:06:00Z

src/jdb_to_nwb/convert_video.py

+    position.loc[:,['x','y']] = fill_missing_gaps(position.loc[:,['x','y']].values)
+
+    # Calculate velocity and acceleration
+    velocity, acceleration = calculate_velocity_acceleration(position['x'].values, position['y'].values,fps = cam_fps, pixel_to_cm = pixelsPerCm)


Suggested change

velocity, acceleration = calculate_velocity_acceleration(position['x'].values, position['y'].values,fps = cam_fps, pixel_to_cm = pixelsPerCm)

velocity, acceleration = calculate_velocity_acceleration(position['x'].values, position['y'].values,fps = cam_fps, pixels_per_cm = pixels_per_cm)

calderast · 2025-01-07T23:15:16Z

src/jdb_to_nwb/convert_video.py

+def detect_and_replace_jumps(coordinates, pixelJumpCutoff):
+    """
+    Detect and replace jumps in the position data that are bigger than pixelJumpCutoff (default30 cm)
+    Jumps are replaced with NaN
+    """
+    n = len(coordinates)
+    jumps = []
+
+    # Calculate Euclidean distances between consecutive points
+    distances = np.linalg.norm(coordinates[1:] - coordinates[:-1], axis=1)
+
+    # Find positions where the distance exceeds the threshold: pixelJumpCutoff
+    jump_indices = np.where(distances > pixelJumpCutoff)[0] + 1


Suggested change

def detect_and_replace_jumps(coordinates, pixelJumpCutoff):

"""

Detect and replace jumps in the position data that are bigger than pixelJumpCutoff (default30 cm)

Jumps are replaced with NaN

"""

n = len(coordinates)

jumps = []

# Calculate Euclidean distances between consecutive points

distances = np.linalg.norm(coordinates[1:] - coordinates[:-1], axis=1)

# Find positions where the distance exceeds the threshold: pixelJumpCutoff

jump_indices = np.where(distances > pixelJumpCutoff)[0] + 1

def detect_and_replace_jumps(coordinates, pixel_jump_cutoff):

"""

Detect and replace jumps in the position data that are bigger than pixel_jump_cutoff (default 30 cm)

Jumps are replaced with NaN

"""

n = len(coordinates)

jumps = []

# Calculate Euclidean distances between consecutive points

distances = np.linalg.norm(coordinates[1:] - coordinates[:-1], axis=1)

# Find positions where the distance exceeds the threshold pixel_jump_cutoff

jump_indices = np.where(distances > pixel_jump_cutoff)[0] + 1

calderast · 2025-01-07T23:53:51Z

src/jdb_to_nwb/convert_video.py

+def calculate_velocity_acceleration(x, y, fps, pixel_to_cm=1):
+    """
+    Calculate velocity and acceleration based on the camera fps and pixelsPerCm
+    """
+    # convert pixel to cm
+    x_cm = x * pixel_to_cm
+    y_cm = y * pixel_to_cm


I was a bit confused about why this was pixel_to_cm - I don't think that should be different from pixels_per_cm? I changed it to be same bc thats how we use it. Also removed the default because I don't think default of 1 makes sense?

Suggested change

def calculate_velocity_acceleration(x, y, fps, pixel_to_cm=1):

"""

Calculate velocity and acceleration based on the camera fps and pixelsPerCm

"""

# convert pixel to cm

x_cm = x * pixel_to_cm

y_cm = y * pixel_to_cm

def calculate_velocity_acceleration(x, y, fps, pixels_per_cm):

"""

Calculate velocity and acceleration based on the camera fps and pixels_per_cm

"""

# convert pixel to cm

x_cm = x * pixels_per_cm

y_cm = y * pixels_per_cm

yangsunhwang and others added 6 commits December 6, 2024 12:20

arranging the video adding functions

fce0a09

After meeting with Ryan notes

bb9c39d

added modules for assigning pixelsPerCm

cef4b8a

Merge branch 'main' into yangsun

1d74934

Merge branch 'main' into yangsun

9ad73ef

finalized docstrings and variables on convert_video.

b45f594

calderast reviewed Dec 20, 2024

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= instead :

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calderast requested changes Jan 7, 2025

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Yang-Sun with adding video and dlc! #15

Yang-Sun with adding video and dlc! #15

yangsunhwang commented Dec 17, 2024

calderast left a comment

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025 •

edited

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calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

calderast Jan 7, 2025

		# Convert arduino timestamps to corresponding photosmetry sample number
		video_timestamps = adjust_video_timestamps(video_timestamps, photometry_start_in_arduino_time)

		# Get pixelsPerCm based on the date of the data collected
		pixelsPerCm = assign_pixels_per_cm(metadata["date"])

-    # Get pixelsPerCm based on the date of the data collected
-    pixelsPerCm = assign_pixels_per_cm(metadata["date"])
+    # If pixels_per_cm exists in metadata, use that value
+    if "pixels_per_cm" in metadata["video"]:
+        PIXELS_PER_CM = metadata["video"]["pixels_per_cm"]
+    # Otherwise, assign it based on the date of the experiment
+    else:
+        PIXELS_PER_CM = assign_pixels_per_cm(metadata["date"])

	x, y, velocity, acceleration = read_dlc(deeplabcut_file_path, phot_dlc = phot_dlc, cutoff = 0.9, cam_fps = 15, pixelsPerCm)
	x, y, velocity, acceleration = read_dlc(deeplabcut_file_path, phot_dlc = phot_dlc, cutoff = 0.9, cam_fps = 15, pixels_per_cm = PIXELS_PER_CM)

	After reading the position data, the position data is used to calculate velocity and acceleration based on the camera fps and pixelsPerCm
	After reading the position data, the position data is used to calculate velocity and acceleration based on the camera fps and pixels_per_cm

	velocity, acceleration = calculate_velocity_acceleration(position['x'].values, position['y'].values,fps = cam_fps, pixel_to_cm = pixelsPerCm)
	velocity, acceleration = calculate_velocity_acceleration(position['x'].values, position['y'].values,fps = cam_fps, pixels_per_cm = pixels_per_cm)

Yang-Sun with adding video and dlc! #15

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Yang-Sun with adding video and dlc! #15

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yangsunhwang commented Dec 17, 2024

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calderast Jan 7, 2025 • edited Loading

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calderast Jan 7, 2025 •

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