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fish_mass.py
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fish_mass.py
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import csv
import numpy as np
from typing import Tuple, List
from laser_parallax import compute_world_points, compute_world_points_from_depths
from array_read_write import read_camera_calibration, read_laser_calibration
from constants import *
from typing import Tuple
import matplotlib.pyplot as plt
import argparse
import os
# Function to take in file name and create a map from file name to
# The key information in the file
def read_csv(csv_file: str) -> dict:
file_map = dict()
# Open up the CSV and begin storing values in map
with open(csv_file, newline='') as csvfile:
reader = csv.reader(csvfile, delimiter=',')
header = next(reader)
for row in reader:
file_map[row[0]] = dict()
for i in range(1, len(header)):
file_map[row[0]][header[i]] = row[i]
return file_map
# Calculate fish length using this
def get_fish_lengths(snout_3d: np.ndarray,
fork_3d: np.ndarray) -> np.ndarray:
# Calculate length of fish using linalg norm
return np.linalg.norm(snout_3d-fork_3d, axis=1)
# Calculate fish mass using species and fish length
def get_fish_masses(fish_lengths: np.ndarray, species: List[str]) -> np.ndarray:
# Temporary return
return np.zeros(fish_lengths.shape)
def prep_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(prog='fish_mass',
description='Calculate fish lengths and masses based on input csv')
parser.add_argument('-c', '--camcalib', help='Camera calibration file', dest='camera_calib_path', required=True)
parser.add_argument('-l', '--lasercalib', help='Laser calibration file', dest='laser_calib_path', required=True)
parser.add_argument('-i', '--input', help='Input csv file', dest='csv_path', required=True)
parser.add_argument('-o', '--output', help='Output csv file', dest='dest_path', required=True)
args = parser.parse_args()
return args
def get_fish_lengths_and_masses(file_name: str,
laser_position: np.ndarray,
laser_orientation: np.ndarray,
camera_params: np.ndarray,
principal_point: np.ndarray) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
file_map = read_csv(file_name)
laser_coords = np.zeros((len(file_map),2))
snout_coords = np.zeros((len(file_map),2))
fork_coords = np.zeros((len(file_map),2))
species_list = []
for i, file in enumerate(file_map):
# Read values from map
laser_x = float(file_map[file]["laser.x"])
laser_y = float(file_map[file]["laser.y"])
snout_x = int(file_map[file]["head.x"])
snout_y = int(file_map[file]["head.y"])
fork_x = int(file_map[file]["tail.x"])
fork_y = int(file_map[file]["tail.y"])
# species = int(file_map[file]["species"])
laser_coords[i] = [laser_x, laser_y]
snout_coords[i] = [snout_x, snout_y]
fork_coords[i] = [fork_x, fork_y]
# species_list.append(species)
laser_3d_coords = compute_world_points(
laser_origin=laser_position,
laser_axis=laser_orientation,
camera_params=camera_params,
image_coordinates=(principal_point - laser_coords)
)
depths = laser_3d_coords[:,2]
snout_3d_coords = compute_world_points_from_depths(
camera_params=camera_params,
image_coordinates=(principal_point - snout_coords),
depths=depths
)
fork_3d_coords = compute_world_points_from_depths(
camera_params=camera_params,
image_coordinates=(principal_point - fork_coords),
depths=depths
)
fish_lengths = get_fish_lengths(snout_3d_coords, fork_3d_coords)
masses = get_fish_masses(fish_lengths, species_list)
return depths, fish_lengths, masses
def main():
args = prep_args()
# Get the map made from the csv file
file_map = read_csv(args.csv_path)
# Get the laser position and orientation from the laser calibration file
laser_position, laser_orientation = read_laser_calibration(args.laser_calib_path)
camera_mat, _ = read_camera_calibration(args.camera_calib_path)
focal_length_mm = camera_mat[0][0] * PIXEL_PITCH_MM
sensor_size_px = np.array([4000,3000])
principal_point = camera_mat[:2,2]
camera_params = (focal_length_mm, sensor_size_px[0], sensor_size_px[1], PIXEL_PITCH_MM)
old_laser_position, old_laser_orientation = read_laser_calibration('trials/9/laser-calibration.dat')
# Prepare to write to the output csv file by creating a 2d array
output_csv = []
output_csv.append(["File_Name", "Length", "Mass"])
fish_depths, fish_lengths, fish_masses = get_fish_lengths_and_masses(file_name=os.fspath(args.csv_path),
laser_position=laser_position,
laser_orientation=laser_orientation,
camera_params=camera_params,
principal_point=principal_point)
for i,file in enumerate(file_map):
output_csv.append([file, fish_lengths[i], fish_masses[i]])
# Write this 2d matrix into a csv file
with open(args.dest_path, 'w') as output_file:
wr = csv.writer(output_file)
wr.writerows(output_csv)
if __name__ == "__main__":
main()