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crop.py
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crop.py
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# Specific script name.
SCRIPT_NAME = 'crop.py'
# Specify script version.
VERSION = 1.0
import argparse
import os
import pandas as pd
import locsutil as lu
MESSAGE = f"""
%s version %s. Requires a path to DNA-PAINT localization file (HDF5), output path,
the coordinates of the top-left corner, and the length of the square side.
Returns cropped DNA-PAINT localization file.
""" % (SCRIPT_NAME, VERSION)
def main():
"""
Crops DNA-PAINT localization with HDBSCAN.
Parameters (user input)
-------
input : str
mask : str
dapi : str, optional
idcol : str, optional
output : str, optional
Returns
-------
None
"""
# Allows user to input parameters on command line.
user_input = argparse.ArgumentParser(description=MESSAGE)
# Inputs file names.
required_named = user_input.add_argument_group('required arguments')
required_named.add_argument('-f', '--input', action='store', required=True, type=str,
help='Input csv drift file name.')
required_named.add_argument('-o', '--output', action='store', required=False, type=str,
help='output file prefix')
# Defines ROI.
required_named.add_argument('-x', '--minx', action='store', required=True, type=int,
help='The X coordinate of the top left corner')
required_named.add_argument('-y', '--miny', action='store', required=True, type=int,
help='The Y coordinate of the top left corner')
required_named.add_argument('-s', '--size', action='store', required=True, type=int,
help='The width/height of the cropping region')
# Optional parameters to crop out.
user_input.add_argument('-z', '--minz', action='store', type=float, default=-9999.9,
help='The minimum z-height of the cropping region, default = disabled')
user_input.add_argument('-Z', '--maxz', action='store', type=float, default=9999.9,
help='The maximum z-height of the cropping region, default = disabled')
args = user_input.parse_args()
in_file = args.input
out_name = args.output
min_x = args.minx
min_y = args.miny
min_z = args.minz
max_z = args.maxz
size = args.size
# Imports locs file.
data = lu.read_locs(in_file)
# Gets working directory path.
work_dir = os.path.dirname(in_file)
# Crops locs file.
out_data = crop_xy(data, min_x, min_y, size)
if min_z and max_z:
out_data = crop_z(out_data, min_z, max_z)
# Imports a yaml file.
yaml_in = in_file.rstrip('hdf5') + 'yaml'
frame_val, height_val, width_val = lu.read_yaml(yaml_in)
# Generates output file name prefix.
file_base = os.path.basename(in_file)
print(file_base)
file_stem = lu.clean_filename(file_base)
if out_name:
out_name = f'{file_stem}_{out_name}'
else:
out_name = f'{file_stem}_cropped'
out_hdf5_name = os.path.join(work_dir, out_name) + '.hdf5'
out_yaml_name = os.path.join(work_dir, out_name) + '.yaml'
# Outputs cropped files.
lu.write_locs(out_data, out_hdf5_name)
lu.write_yaml(frame_val, size, size, out_yaml_name)
def crop_xy(locs_data: pd.DataFrame, min_x: float, min_y: float, width: float) -> pd.DataFrame:
"""
Crops localization data using given x & y coordinates and width.
For Picasso localization data, x and y are in camera-pixel scale.
top-left : (mix_x, min_y),
top-right : (mix_x + width, min_y),
bottom-left : (mix_x, min_y + width),
bottom-right : (mix_x + width, min_y + width)
Parameters
----------
locs_data : pd.DataFrame
Localization data.
min_x : float
x of the top-left corner of the cropping square.
min_y : float
y of the top-left corner of the cropping square.
width : float
Width of the cropping square.
Returns
-------
cropped : pd.DataFrame
"""
max_x = min_x + width
max_y = min_y + width
cropped = locs_data.copy()
cropped = cropped[(cropped['x'] >= min_x) & (cropped['x'] <= max_x)]
cropped = cropped[(cropped['y'] >= min_y) & (cropped['y'] <= max_y)]
cropped['x'] -= min_x
cropped['y'] -= min_y
return cropped
def crop_z(locs_data: pd.DataFrame, min_z: float, max_z: float) -> pd.DataFrame:
"""
Crops localization data using given a z height range.
Parameters
----------
locs_data : pd.DataFrame
Localization data.
min_z : float
max_z : float
Returns
-------
cropped : pd.DataFrame
"""
cropped = locs_data.copy()
cropped = cropped[(cropped['z'] >= min_z) & (cropped['z'] <= max_z)]
return cropped
if __name__ == '__main__':
main()