Mercurial > repos > galaxyp > zeiss_lmd_converter

comparison tabular_to_ZeissLMDtext.py @ 0:f17bc16fefcf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter commit 17fc7ee7911e0b875aaed5be4a129cfea208c76f
author galaxyp
date Mon, 01 Jul 2024 14:07:46 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:f17bc16fefcf
1 import argparse
2
3 from shapely.geometry import Polygon
4
5
6 def tabular_to_text(input_file, text_file):
7 """
8 Converts tabular coordinate data from Galaxy into a formatted text file which is readable for the LMD.
9
10 This function reads tabular data from an input file, processes it to form a closed polygon, calculates the area
11 of the polygon, and writes the formatted information to an output text file.
12
13 Parameters:
14 input_file (str): Path to the input file containing tabular coordinate data.
15 The file should have a header and each line should contain x and y coordinates separated by a tab.
16 text_file (str): Path to the output text file where the formatted information will be written.
17
18 The output text file will contain:
19 - Header information
20 - A section with metadata including version, date, and time
21 - A section with details of the polygon including type, color, thickness, number, cutshot, area, comment,
22 and coordinates.
23 """
24 coordinates = []
25 with open(input_file, 'r') as f:
26 next(f) # Skip the header
27 for line in f:
28 x, y = map(float, line.strip().split('\t'))
29 coordinates.append([x, y])
30
31 coordinates.append(coordinates[0]) # Close the polygon by repeating the first point as the last point
32 area = Polygon(coordinates).area
33
34 with open(text_file, 'w') as f:
35 f.write("PALMRobo Elements\n")
36 f.write("Version:\tV 4.6.0.4\n")
37 f.write("Date, Time:\t13.02.2024\t16:06:32\n")
38 f.write("\nMICROMETER\nElements :\n\nType\tColor\tThickness\tNo\tCutShot\tArea\tComment\tCoordinates\n\n")
39 f.write(f"Freehand\tgreen\t0\t7\t0,0\t{area}\tROI imported from tabular data\n")
40
41 for i in range(0, len(coordinates), 5):
42 for j in range(5):
43 if i + j < len(coordinates):
44 x, y = coordinates[i + j]
45 f.write(f"\t{x},{y}")
46 f.write("\n.")
47
48
49 if __name__ == '__main__':
50 parser = argparse.ArgumentParser(description="Convert tabular coordinate data into a formatted text file")
51 parser.add_argument('--input', type=str, required=True, help='Path to the input tabular file')
52 parser.add_argument('--output', type=str, required=True, help='Path to the output text file')
53 args = parser.parse_args()
54
55 tabular_to_text(args.input, args.output)