VasLem

check_for_venv() {
    	DIR_NAME=$PWD
    	VENVLOC=
    	while [ "$DIR_NAME" != "/" ]; do
        	if [ -e "$DIR_NAME/bin/python" ] && [ -e "$DIR_NAME/bin/activate" ]; then
            		VENVLOC="$DIR_NAME"
			_VENV_NAME=$(basename $DIR_NAME)
            		break
		elif [ -e "$DIR_NAME/.venv/bin/python" ] && [ -e "$DIR_NAME/.venv/bin/activate" ] ; then

VasLem

"""Defines a fixture that does the following:
- Create an asymmetric way to read and write files.
If to write files, redirect to TEST_DATA_DIRS corresponding folder.
If to read files, check whether TEST_DATA_DIRS corresponding file exists there and read from there, else read from DATA_DIR.
TEST_DATA_ONLY_DIRS are directly read from the TEST_DATA_DIR
If files end with IGNORE_EXTENSIONS, read from DATA_DIRS

Only path strings are currenly supported, not Path variables!

 (**NOTICE**: System builtins are also overriden)

VasLem

from typing import List, Union, cast

from torch import nn
from torch.nn import BCEWithLogitsLoss, MaxPool2d, functional


class ResBlock(nn.Module):
    def __init__(self, in_channels, out_channels, doShortcut=True):
        super().__init__()
        inter_channels = round((in_channels + out_channels) / 2)

VasLem

form typing import List
from patch import Patch
def iou(patch, patches: List[Patch]):
    # commpute IoU between a patch and a list of patches
    ref_mask = patch.mask
    ref_box = patch.bbox
    ref_mask_size = np.sum(ref_mask > 0)
    seg_ious = []
    for patch in patches:
        reg_box = patch.bbox

VasLem

# Assumes ffmpeg has been installed in conda environment
# Assumes Linux environment.

import os
import shutil
import subprocess

import cv2
import numpy as np

VasLem

import numpy as np
import cv2    
import math
from bezier.curve import Curve

def generate_curved_polygon(
    num_sides: int,
    radius: float,
    orientation: int = 0,
    side_curvature=0.1,

VasLem

#!/usr/bin/env python
# %%
import pandas as pd
import numpy as np
import requests
import tarfile
import tempfile
import os
from math import ceil
from tqdm.auto import tqdm

VasLem

#!/bin/bash
# required: bedtools in $PATH
print_help(){
echo -e "
1st pos. argument: the bed path to annotate
2nd pos. argument: the bed path to get the annotations from
3rd pos. argument: the output filename
4th pos. argument:  whether the output has headers (1) or not (0)
5th optional pos. argument: the prefix to add to the annotated columns, if header to be output
"

VasLem

#!/bin/bash
# required: bedtools and bedops in $PATH
print_help(){
echo -e "
1st pos. argument: the bed paths space separated
2nd pos. argument: the bed paths ids, space separated, with size equal to bed paths
3rd pos. argument: the output filename
4rth pos.argument: whether the inputs have headers (1) or not (0)
"
}

VasLem

#!/usr/bin/env python
from tqdm import tqdm
import sys
import contextlib
import logging
from typing import Literal

LOGGER = logging.getLogger("bed_annotate")