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Integrate generation of structural formulas as plots

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This commit is contained in:
Matthias Bisping 2023-02-15 19:31:00 +01:00
parent 0e7791394f
commit 66c65ce900
9 changed files with 184 additions and 17 deletions
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1
cv_analysis/locations.py
View File

@ -11,3 +11,4 @@ TEST_DATA_DIR = TEST_DIR_PATH / "data"
TEST_DATA_DIR_DVC = TEST_DIR_PATH / "data.dvc"
TEST_DATA_SYNTHESIS_DIR = TEST_DATA_DIR / "synthesis"
TEST_PAGE_TEXTURES_DIR = TEST_DATA_SYNTHESIS_DIR / "paper"
TEST_SMILES_FILE = TEST_DATA_SYNTHESIS_DIR / "smiles.csv"

5
cv_analysis/logging.py
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@ -13,7 +13,7 @@ debug_logger = loguru.logger
debug_logger.add(
sink=sys.stderr,
format="<blue>{time:YYYY-MM-DD at HH:mm:ss}</blue> | <level>{level: <8}</level> | <cyan>{name}</cyan>: <level>{message}</level>",
level="TRACE",
level="DEBUG",
)
dev_logger = loguru.logger
@ -31,6 +31,9 @@ prod_logger.add(
enqueue=True,
)
# logger.remove()
# logger.add(sink=sys.stderr, level="DEBUG", enqueue=True)
def __log(logger, level: str, enters=True, exits=True) -> Callable:
print_func = get_print_func(logger, level)

4
cv_analysis/utils/rectangle.py
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@ -51,6 +51,10 @@ class Rectangle:
def coords(self):
return [self.x1, self.y1, self.x2, self.y2]
@property
def size(self):
return self.width, self.height
def __hash__(self):
return hash((self.x1, self.y1, self.x2, self.y2))

40
poetry.lock generated
View File

@ -2229,6 +2229,18 @@ opencv-python-headless = ">=4.0.1"
scikit-learn = ">=0.19.1"
typing-extensions = "*"
[[package]]
name = "rdkit"
version = "2022.9.4"
description = "A collection of chemoinformatics and machine-learning software written in C++ and Python"
category = "main"
optional = false
python-versions = "*"
[package.dependencies]
numpy = "*"
Pillow = "*"
[[package]]
name = "requests"
version = "2.28.1"
@ -2862,7 +2874,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools"
[metadata]
lock-version = "1.1"
python-versions = "~3.8"
content-hash = "117d9fceef40b37d126a7c2e47125c74373307e1f9a0f0ae82fc9e5e21295f25"
content-hash = "45539080e4964adfec7aad366e5ae67e25659afa188f4da882f93fe4f313fe36"
[metadata.files]
aiohttp = [
@ -4500,6 +4512,32 @@ qudida = [
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{file = "qudida-0.0.4.tar.gz", hash = "sha256:db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8"},
]
rdkit = [
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1
pyproject.toml
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@ -31,6 +31,7 @@ PyMuPDF = "^1.19.6"
pdf2img = {git = "ssh://git@git.iqser.com:2222/rr/pdf2image.git", branch = "master"}
pyinfra = {git = "ssh://git@git.iqser.com:2222/rr/pyinfra.git", branch = "master"}
loguru = "^0.6.0"
rdkit = "^2022.9.4"
[tool.poetry.group.build.dependencies]
pytest = "^7.0.1"

141
synthesis/formula.py
View File

@ -1,16 +1,129 @@
import argparse
# Draw molecular structures from smiles. Adapted from https://github.com/neeraj-j/molecules
from itertools import islice
from typing import List, Iterable
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument()
args = parser.parse_args()
return args
def main(args):
pass
import numpy as np
import pandas as pd
from PIL.Image import Image
from funcy import first, retry, keep
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem import FunctionalGroups
if __name__ == "__main__":
main(parse_args())
from cv_analysis.locations import TEST_SMILES_FILE
from cv_analysis.logging import debug_log, logger
class StructuralFormulaImageGenerator:
def __init__(self, width=None, height=None):
self.width = width
self.height = height
self.templates = collect_templates()
self.functional_groups = self.templates.keys()
@debug_log()
def generate_images_from_smiles(self, smiles: List[str], max_images_per_functional_group=1) -> Iterable[Image]:
yield from self.generate_images_for_functional_groups(
smiles,
max_images_per_functional_group=max_images_per_functional_group,
)
@debug_log()
def generate_images_for_functional_groups(self, smiles: List[str], max_images_per_functional_group):
for functional_group in self.functional_groups:
smiles = iter(smiles)
g = self.generate_images_for_functional_group(smiles, functional_group)
yield from islice(keep(g), max_images_per_functional_group)
def generate_images_for_functional_group(self, smiles: Iterable[str], functional_group: str):
try:
yield from self.__generate_images_for_functional_group(smiles, functional_group)
except ValueError:
pass
@debug_log()
@retry(10, errors=ValueError)
def __generate_images_for_functional_group(self, smiles: Iterable[str], functional_group: str):
AllChem.Compute2DCoords(self.templates[functional_group])
for smile in smiles:
try:
image = self.make_image(smile, functional_group)
yield image
except ValueError: # SMILE does not match functional group
raise
@debug_log()
def make_image(self, smile: str, functional_group: str):
mol = Chem.MolFromSmiles(smile)
AllChem.GenerateDepictionMatching2DStructure(mol, self.templates[functional_group])
side_length = np.random.randint(70, 400)
width = self.width or side_length
height = self.height or side_length
image: Image = Draw.MolToImage(
mol,
size=(width, height),
kekulize=flip_a_coin(),
wedgeBonds=flip_a_coin(),
)
image.putalpha(255)
return image
@debug_log()
def flip_a_coin():
return bool(np.random.randint(0, 2))
@debug_log()
def collect_templates():
functional_groups = FunctionalGroups.BuildFuncGroupHierarchy()
group_name_2_pattern = dict(stream_label_pattern_pairs(functional_groups))
return group_name_2_pattern
@debug_log()
def stream_label_pattern_pairs(functional_groups):
for functional_group in functional_groups:
yield functional_group.label, functional_group.pattern
yield from stream_label_pattern_pairs(functional_group.children)
@debug_log()
def generate_image_of_structural_formula(smiles_file=None, size=None):
"""Generate images of formulas from SMILE encoded formulas.
Args:
smiles_file: CSV file with column "smiles". Each row contains a SMILE encoded formula.
size: width, height
Returns:
PIL.Image.Image: Image of a formula.
"""
logger.info(f"Generating structural formula images from {smiles_file}")
return first(generate_images_of_structural_formulas(smiles_file, size=size))
@debug_log()
def generate_images_of_structural_formulas(smiles_file=None, size=None):
"""Generate an image of a formula from SMILE encoded formulas.
Args:
smiles_file: CSV file with column "smiles". Each row contains a SMILE encoded formula.
size: width, height
Yields:
PIL.Image.Image: Image of a formula.
"""
size = size or (None, None)
smiles_file = smiles_file or TEST_SMILES_FILE
smiles = pd.read_csv(smiles_file).sample(frac=1).drop_duplicates().smiles
yield from StructuralFormulaImageGenerator(*size).generate_images_from_smiles(smiles)
# generate_image_of_structural_formula().show()

6
synthesis/segment/plot.py
View File

@ -11,6 +11,7 @@ from matplotlib.colors import ListedColormap
from cv_analysis.utils.geometric import is_square_like, is_wide, is_tall
from cv_analysis.utils.image_operations import superimpose
from cv_analysis.utils.rectangle import Rectangle
from synthesis.formula import generate_image_of_structural_formula
from synthesis.randomization import rnd, probably, maybe
from synthesis.segment.random_content_rectangle import RandomContentRectangle
from synthesis.text.text import generate_random_words
@ -39,6 +40,7 @@ class RandomPlot(RandomContentRectangle):
self.generate_random_histogram,
self.generate_random_pie_chart,
self.generate_random_heat_map,
self.generate_random_structural_formula
]
)
elif is_wide(rectangle):
@ -141,6 +143,10 @@ class RandomPlot(RandomContentRectangle):
plot_kwargs=self.generate_plot_kwargs(keywords=["a"]),
)
def generate_random_structural_formula(self, rectangle: Rectangle):
image = generate_image_of_structural_formula(size=rectangle.size)
self.content = image if not self.content else superimpose(self.content, image)
def generate_plot_kwargs(self, keywords=None):
kwargs = {

1
test/conftest.py
View File

@ -6,6 +6,7 @@ pytest_plugins = [
"test.fixtures.table_parsing",
"test.fixtures.figure_detection",
"test.fixtures.data",
"test.fixtures.formula",
"test.fixtures.page_generation.page",
]

2
test/page_generation_test.py
View File

@ -15,5 +15,5 @@ def test_blank_page(page_with_content):
def draw_boxes(page: Image, boxes: Iterable[Rectangle]):
from cv_analysis.utils.drawing import draw_rectangles
page = draw_rectangles(page, boxes, filled=False, annotate=True)
# page = draw_rectangles(page, boxes, filled=False, annotate=True)
show_image(page, backend="pil")