diff --git a/tools/points2binaryimage/points2binaryimage.py b/tools/points2binaryimage/points2binaryimage.py index a5815f9f..dabce37b 100644 --- a/tools/points2binaryimage/points2binaryimage.py +++ b/tools/points2binaryimage/points2binaryimage.py @@ -1,36 +1,75 @@ import argparse import os import warnings +from typing import List import numpy as np import pandas as pd +import scipy.ndimage as ndi import skimage.io -def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, swap_xy=False): +def find_column(df: pd.DataFrame, candidates: List[str]) -> str: + """ + Returns tje column name present in `df` and the list of `candidates`. - img = np.zeros(shape, dtype=np.int16) + Raises: + KeyError: If there is no candidate column name present in `df`, or more than one. + """ + intersection = frozenset(df.columns) & frozenset(candidates) + if len(intersection) == 0: + raise KeyError(f'No such column: {", ".join(candidates)}') + elif len(intersection) > 1: + raise KeyError(f'The column names {", ".join(intersection)} are ambiguous') + else: + return next(iter(intersection)) + + +def points2binaryimage(point_file, out_file, shape, has_header=False, swap_xy=False, bg_value=0, fg_value=0xffff): + + img = np.full(shape, dtype=np.uint16, fill_value=bg_value) if os.path.exists(point_file) and os.path.getsize(point_file) > 0: + + # Read the tabular file with information from the header if has_header: - df = pd.read_csv(point_file, skiprows=1, header=None, delimiter="\t") + df = pd.read_csv(point_file, delimiter='\t') + pos_x_column = find_column(df, ['pos_x', 'POS_X']) + pos_y_column = find_column(df, ['pos_y', 'POS_Y']) + pos_x_list = df[pos_x_column].round().astype(int) + pos_y_list = df[pos_y_column].round().astype(int) + assert len(pos_x_list) == len(pos_y_list) + try: + radius_column = find_column(df, ['radius', 'RADIUS']) + radius_list = df[radius_column] + except KeyError: + radius_list = [0] * len(pos_x_list) + + # Read the tabular file without header else: - df = pd.read_csv(point_file, header=None, delimiter="\t") - - for i in range(0, len(df)): - a_row = df.iloc[i] - if int(a_row[0]) < 0 or int(a_row[1]) < 0: - raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1])) - - if swap_xy: - if img.shape[0] <= int(a_row[0]) or img.shape[1] <= int(a_row[1]): - raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1])) - else: - img[int(a_row[1]), int(a_row[0])] = 32767 + df = pd.read_csv(point_file, header=None, delimiter='\t') + pos_x_list = df[0].round().astype(int) + pos_y_list = df[1].round().astype(int) + assert len(pos_x_list) == len(pos_y_list) + radius_list = [0] * len(pos_x_list) + + # Optionally swap the coordinates + if swap_xy: + pos_x_list, pos_y_list = pos_y_list, pos_x_list + + # Perform the rasterization + for y, x, radius in zip(pos_y_list, pos_x_list, radius_list): + + if y < 0 or x < 0 or y >= shape[0] or x >= shape[1]: + raise IndexError(f'The point x={x}, y={y} exceeds the bounds of the image (width: {shape[1]}, height: {shape[0]})') + + if radius > 0: + mask = np.ones(shape, dtype=bool) + mask[y, x] = False + mask = (ndi.distance_transform_edt(mask) <= radius) + img[mask] = fg_value else: - if img.shape[0] <= int(a_row[1]) or img.shape[1] <= int(a_row[0]): - raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[1]), int(a_row[0]), shape[0], shape[1])) - else: - img[int(a_row[0]), int(a_row[1])] = 32767 + img[y, x] = fg_value + else: raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error? @@ -51,4 +90,4 @@ def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, args = parser.parse_args() # TOOL - points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, swap_xy=args.swap_xy) + points2binaryimage(args.point_file.name, args.out_file, (args.shapey, args.shapex), has_header=args.has_header, swap_xy=args.swap_xy) diff --git a/tools/points2binaryimage/points2binaryimage.xml b/tools/points2binaryimage/points2binaryimage.xml index 7e5ab3d0..d890ef35 100644 --- a/tools/points2binaryimage/points2binaryimage.xml +++ b/tools/points2binaryimage/points2binaryimage.xml @@ -3,8 +3,8 @@ creators.xml tests.xml - 0.2 - 3 + 0.3 + 0 @@ -46,22 +46,39 @@ - - + + + + + + + + + + **Converts a tabular list of points to a binary image by rasterizing the point coordinates.** The created image is a single-channel image with 16 bits per pixel (unsigned integer). - The points are rasterized with value 32767 (white). + The points are rasterized with value 65535 (white). Pixels not corresponding to any points in the tabular file are assigned the value 0 (black). + The tabular list of points can either be header-less. + In this case, the first and second columns are expected to be the X and Y coordinates, respectively. + Otherwise, if a header is present, it is searched for the following column names: + + - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates. + - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates. + - If a ``radius`` or ``RADIUS`` column is present, + then the points will be rasterized as circles of the corresponding radii. + 10.1016/j.jbiotec.2017.07.019 diff --git a/tools/points2binaryimage/test-data/input2.tsv b/tools/points2binaryimage/test-data/input2.tsv new file mode 100644 index 00000000..47efffa6 --- /dev/null +++ b/tools/points2binaryimage/test-data/input2.tsv @@ -0,0 +1,39 @@ +frame pos_x pos_y scale radius intensity +1 85 32 1.33 3.77 18807.73 +1 190 25 1.78 5.03 24581.44 +1 137 26 1.44 4.09 19037.59 +1 63 42 1.44 4.09 22390.80 +1 107 44 1.33 3.77 23429.96 +1 61 27 1.56 4.40 18052.18 +1 158 39 1.44 4.09 18377.02 +1 190 14 1.33 3.77 18548.86 +1 182 33 1.78 5.03 26467.79 +1 39 39 1.44 4.09 14782.43 +1 169 26 1.33 3.77 14203.41 +1 61 54 1.33 3.77 23248.06 +1 95 52 1.33 3.77 21480.71 +1 23 60 1.89 5.34 25203.43 +1 84 24 1.56 4.40 16630.57 +1 121 47 1.67 4.71 15459.11 +1 66 49 1.11 3.14 23858.07 +1 115 36 2.00 5.66 16389.10 +1 55 51 1.33 3.77 23548.90 +1 130 72 1.67 4.71 15769.02 +1 117 23 1.33 3.77 16763.14 +1 45 52 1.56 4.40 22877.61 +1 36 71 1.56 4.40 20780.96 +1 78 17 1.33 3.77 16844.51 +1 101 38 1.56 4.40 21376.59 +1 147 31 1.78 5.03 16597.14 +1 163 55 2.00 5.66 18301.54 +1 164 23 1.33 3.77 17073.82 +1 150 24 1.56 4.40 15440.02 +1 151 67 1.78 5.03 18419.96 +1 26 53 2.00 5.66 20586.01 +1 79 62 1.33 3.77 15232.88 +1 69 17 1.11 3.14 15601.83 +1 83 52 1.33 3.77 18315.00 +1 16 54 2.00 5.66 22140.66 +1 166 61 1.78 5.03 18488.78 +1 163 43 1.44 4.09 16925.49 +1 130 53 1.78 5.03 15101.96 diff --git a/tools/points2binaryimage/test-data/output1.original.tif b/tools/points2binaryimage/test-data/output1.original.tif new file mode 100644 index 00000000..99a69a37 Binary files /dev/null and b/tools/points2binaryimage/test-data/output1.original.tif differ diff --git a/tools/points2binaryimage/test-data/output1.tif b/tools/points2binaryimage/test-data/output1.tif index 99a69a37..4a946253 100644 Binary files a/tools/points2binaryimage/test-data/output1.tif and b/tools/points2binaryimage/test-data/output1.tif differ diff --git a/tools/points2binaryimage/test-data/output2.tif b/tools/points2binaryimage/test-data/output2.tif new file mode 100644 index 00000000..922cd0d5 Binary files /dev/null and b/tools/points2binaryimage/test-data/output2.tif differ