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Merge pull request #133 from kostrykin/points2binaryimage/dev
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Update the `points2binaryimage` tool
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@kostrykin
kostrykin authored Sep 25, 2024
2 parents f1b9207 + c0434cb commit a3c77a7
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85 changes: 62 additions & 23 deletions tools/points2binaryimage/points2binaryimage.py
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@@ -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, invert_xy=False):
def find_column(df: pd.DataFrame, candidates: List[str]) -> str:
"""
Returns the 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 invert_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?

Expand All @@ -41,14 +80,14 @@ def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False,

if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('point_file', type=argparse.FileType('r'), help='label file')
parser.add_argument('point_file', type=argparse.FileType('r'), help='point file')
parser.add_argument('out_file', type=str, help='out file (TIFF)')
parser.add_argument('shapex', type=int, help='shapex')
parser.add_argument('shapey', type=int, help='shapey')
parser.add_argument('--has_header', dest='has_header', default=False, help='set True if CSV has header')
parser.add_argument('--invert_xy', dest='invert_xy', default=False, help='invert x and y in CSV')
parser.add_argument('--has_header', dest='has_header', default=False, help='set True if point file has header')
parser.add_argument('--swap_xy', dest='swap_xy', default=False, help='Swap X and Y coordinates')

args = parser.parse_args()

# TOOL
points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy)
points2binaryimage(args.point_file.name, args.out_file, (args.shapey, args.shapex), has_header=args.has_header, swap_xy=args.swap_xy)
76 changes: 50 additions & 26 deletions tools/points2binaryimage/points2binaryimage.xml
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Expand Up @@ -2,8 +2,9 @@
<description></description>
<macros>
<import>creators.xml</import>
<token name="@TOOL_VERSION@">0.2</token>
<token name="@VERSION_SUFFIX@">3</token>
<import>tests.xml</import>
<token name="@TOOL_VERSION@">0.3</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<creator>
<expand macro="creators/bmcv" />
Expand All @@ -15,45 +16,68 @@
<xref type="bio.tools">galaxy_image_analysis</xref>
</xrefs>
<requirements>
<requirement type="package" version="0.14.2">scikit-image</requirement>
<requirement type="package" version="1.15.4">numpy</requirement>
<requirement type="package" version="0.23.4">pandas</requirement>
<requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
<requirement type="package" version="2.5.2">python-dateutil</requirement>
<requirement type="package" version="0.15.1">tifffile</requirement>
<requirement type="package" version="0.21">scikit-image</requirement>
<requirement type="package" version="1.26.4">numpy</requirement>
<requirement type="package" version="1.2.4">pandas</requirement>
<requirement type="package" version="2024.6.18">tifffile</requirement>
</requirements>
<command detect_errors="aggressive">
<![CDATA[
python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy
]]>
</command>
<command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/points2binaryimage.py'
'$input'
'$output'
$shapex
$shapey
$has_header
$swap_xy
]]></command>
<inputs>
<param name="input" type="data" format="tabular" label="CSV point file"/>
<param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" />
<param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" />
<param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" />
<param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" />
<param name="input" type="data" format="tabular" label="Tabular list of points"/>
<param name="shapex" type="integer" value="500" min="1" label="Width of output image" />
<param name="shapey" type="integer" value="500" min="1" label="Height of output image" />
<param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of points has header" />
<param name="swap_xy" type="boolean" checked="false" falsevalue="" truevalue="--swap_xy True" optional="true" label="Swap X and Y coordinates" />
</inputs>
<outputs>
<data name="output" format="tiff" />
</outputs>
<tests>
<!-- TSV without header -->
<test>
<param name="input" value="points.tsv" />
<param name="shapex" value="20" />
<param name="shapey" value="30" />
<param name="input" value="input1.tsv" />
<param name="shapex" value="30" />
<param name="shapey" value="20" />
<param name="has_header" value="false" />
<param name="invert_xy" value="true" />
<output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/>
<param name="swap_xy" value="true" />
<expand macro="tests/binary_image_diff" name="output" value="output1.tif" ftype="tiff" />
</test>
<!-- TSV with header -->
<test>
<param name="input" value="input2.tsv" />
<param name="shapex" value="205" />
<param name="shapey" value="84" />
<param name="has_header" value="true" />
<param name="swap_xy" value="false" />
<expand macro="tests/binary_image_diff" name="output" value="output2.tif" ftype="tiff" />
</test>
</tests>
<help>

This tool converts a CSV list of points to a binary image by rasterizing the point coordinates.
**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).
Pixels not corresponding to any points in the CSV are assigned the value 0 (black).
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.

</help>
<citations>
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0 ...s/points2binaryimage/test-data/points.tsv → ...s/points2binaryimage/test-data/input1.tsv
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39 changes: 39 additions & 0 deletions tools/points2binaryimage/test-data/input2.tsv
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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
0 tools/points2binaryimage/test-data/out.tiff → ...inaryimage/test-data/output1.original.tif
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1 change: 1 addition & 0 deletions tools/points2binaryimage/tests.xml
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../../macros/tests.xml

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