diff --git a/tools/zeiss_lmd_converter/.shed.yml b/tools/zeiss_lmd_converter/.shed.yml new file mode 100644 index 000000000..6638443eb --- /dev/null +++ b/tools/zeiss_lmd_converter/.shed.yml @@ -0,0 +1,9 @@ +categories: + - Proteomics +description: Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems +long_description: | + This tool is part of a workflow that allows to use tissue anontations in geojson format from machine learning based imaging software like QuPath and HaloAI and transform these annotation coordinates into a text format readable by Zeiss laser-capture microdissection systems +owner: galaxyp +remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter +homepage_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter +type: unrestricted diff --git a/tools/zeiss_lmd_converter/tabular_to_ZeissLMDtext.py b/tools/zeiss_lmd_converter/tabular_to_ZeissLMDtext.py new file mode 100644 index 000000000..64583726e --- /dev/null +++ b/tools/zeiss_lmd_converter/tabular_to_ZeissLMDtext.py @@ -0,0 +1,53 @@ +import argparse +from shapely.geometry import Polygon + +def tabular_to_text(input_file, text_file): + """ + Converts tabular coordinate data from Galaxy into a formatted text file which is readable for the LMD. + + This function reads tabular data from an input file, processes it to form a closed polygon, calculates the area + of the polygon, and writes the formatted information to an output text file. + + Parameters: + input_file (str): Path to the input file containing tabular coordinate data. + The file should have a header and each line should contain x and y coordinates separated by a tab. + text_file (str): Path to the output text file where the formatted information will be written. + + The output text file will contain: + - Header information + - A section with metadata including version, date, and time + - A section with details of the polygon including type, color, thickness, number, cutshot, area, comment, + and coordinates. + """ + coordinates = [] + with open(input_file, 'r') as f: + next(f) # Skip the header + for line in f: + x, y = map(float, line.strip().split('\t')) + coordinates.append([x, y]) + + coordinates.append(coordinates[0]) # Close the polygon by repeating the first point as the last point + area = Polygon(coordinates).area + + with open(text_file, 'w') as f: + f.write("PALMRobo Elements\n") + f.write("Version:\tV 4.6.0.4\n") + f.write("Date, Time:\t13.02.2024\t16:06:32\n") + f.write("\nMICROMETER\nElements :\n\nType\tColor\tThickness\tNo\tCutShot\tArea\tComment\tCoordinates\n\n") + f.write(f"Freehand\tgreen\t0\t7\t0,0\t{area}\tROI imported from tabular data\n") + + for i in range(0, len(coordinates), 5): + for j in range(5): + if i + j < len(coordinates): + x, y = coordinates[i + j] + f.write(f"\t{x},{y}") + f.write("\n.") + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description="Convert tabular coordinate data into a formatted text file") + parser.add_argument('--input', type=str, required=True, help='Path to the input tabular file') + parser.add_argument('--output', type=str, required=True, help='Path to the output text file') + args = parser.parse_args() + + tabular_to_text(args.input, args.output) + diff --git a/tools/zeiss_lmd_converter/test-data/Zeiss_converted_file.txt b/tools/zeiss_lmd_converter/test-data/Zeiss_converted_file.txt new file mode 100644 index 000000000..eec5993c5 --- /dev/null +++ b/tools/zeiss_lmd_converter/test-data/Zeiss_converted_file.txt @@ -0,0 +1,345 @@ +PALMRobo Elements +Version: V 4.6.0.4 +Date, Time: 13.02.2024 16:06:32 + +MICROMETER +Elements : + +Type Color Thickness No CutShot Area Comment Coordinates + +Freehand green 0 7 0,0 5331.660000000684 ROI imported from tabular data + 70811.7,31281.3 70811.2,31281.3 70810.8,31281.3 70810.3,31281.3 70809.8,31281.3 +. 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+ + + + + + + + + + + This tool reads tabular data containing x and y coordinates, processes it to form a closed polygon, + calculates the polygon's area, and writes a formatted text file readable by the PALM RoboSoftware of Zeiss laser-capture microdissection systems. + + + + @Misc{shapely2007, + author = {Sean Gillies and others}, + organization = {toblerity.org}, + title = {Shapely: manipulation and analysis of geometric objects}, + year = {2007--}, + url = "https://github.com/Toblerity/Shapely"} + + +