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| import re | |
| import subprocess | |
| from experimental import Plate, Image, create_companion | |
| # https://github.com/ome/ome-model/blob/master/ome_model/experimental.py | |
| # (pip install ome-model) | |
| # R44821_160620150002i3t001A06f01d2.ome.tif | |
| pat = re.compile(r"^(?P<plate>.*?)i3t(?P<timepoint>\d+)(?P<wellrow>\w)(?P<wellcol>\d{2,})f(?P<field>\d{2})d(?P<channel>\d)\.*") | |
| plate_name = "R44821_160620150002" | |
| order = "XYCZT" | |
| img_x = 1104 | |
| img_y = 1104 | |
| size_z = 1 | |
| size_c = 1 | |
| pix_type = "uint16" | |
| # Read the whole file | |
| files = [] | |
| with open("image-file-listing.txt") as fp: | |
| line = fp.readline() | |
| while line: | |
| files.append(line.strip()) | |
| line = fp.readline() | |
| # Get number of rows, columns and timepoints | |
| n_rows = set() | |
| n_cols = set() | |
| n_timepoints = set() | |
| for file in files: | |
| m = pat.match(file).groupdict() | |
| n_rows.add(m['wellrow']) | |
| n_cols.add(int(m['wellcol'])) | |
| n_timepoints.add(int(m['timepoint'])) | |
| n_rows = len(n_rows) | |
| n_cols = len(n_cols) | |
| n_timepoints = len(n_timepoints) | |
| # assemble 5d images (key: wellrow|wellcol) | |
| images = {} | |
| for file in files: | |
| m = pat.match(file).groupdict() | |
| key = f"{m['wellrow']}|{m['wellcol']}" | |
| if not key in images: | |
| images[key] = Image(key, img_x, img_y, size_z, size_c, n_timepoints, order=order, type=pix_type) | |
| images[key].add_channel(samplesPerPixel=1) | |
| images[key].add_plane(c=0, t=int(m['timepoint'])-1, z=0) | |
| images[key].add_tiff(file, c=0, z=0, t=int(m['timepoint'])-1, planeCount=1) | |
| # assemble plate | |
| plate = Plate(plate_name, n_rows, n_cols) | |
| row_indices = "ABCDEFGHIJKLMNOPQRSTUVWXYZ" | |
| for well_pos, image in images.items(): | |
| row = well_pos.split("|")[0] | |
| col = int(well_pos.split("|")[1])-1 | |
| well = plate.add_well(row_indices.index(row), col) | |
| well.add_wellsample(0, image) | |
| # write companion file | |
| companion_file = "{}.companion.ome".format(plate_name) | |
| create_companion(plates=[plate], out=companion_file) | |
| # Indent XML for readability | |
| proc = subprocess.Popen( | |
| ['xmllint', '--format', '-o', companion_file, companion_file], | |
| stdin=subprocess.PIPE, | |
| stdout=subprocess.PIPE) | |
| (output, error_output) = proc.communicate() |
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