shahpnmlab

from pathlib import Path
import imodmodel
import starfile
import pandas as pd
import numpy as np

# Create optics dataframe
df_optics = pd.DataFrame({
    'rlnOpticsGroup': [1],
    'rlnOpticsGroupName': ["OpticsGroup1"],

shahpnmlab

import numpy as np
import starfile

XDIM = 378
YDIM = 378
ZDIM = 228

df = starfile.read("gs07_ts_003_8.00Apx_emd_13474_clean.star")
xyz_headings = [f'rlnCoordinate{axis}' for axis in 'XYZ']
xyz_headings.append('rlnAutopickFigureOfMerit')

shahpnmlab

from pathlib import Path
import mdocfile
import shutil
import typer
import logging
from typing import Optional

# Configure logging
logging.basicConfig(
    level=logging.INFO,

shahpnmlab

import starfile
import pandas as pd

df_optics = pd.DataFrame({
    'rlnOpticsGroup': [1],
    "rlnOpticsGroupName": ["OpticsGroup1"],
    'rlnSphericalAberration': [2.7],
    'rlnVoltage': [300],
    'rlnImagePixelSize': [5],
    'rlnImageDimensionality': [3]

shahpnmlab

import typer
import logging
from pathlib import Path
import imodmodel
import numpy as np
import matplotlib.path as mplPath
import mrcfile
from scipy.interpolate import interp1d

app = typer.Typer(add_completion=False)

shahpnmlab

import starfile
import typer
from pathlib import Path
import subprocess
import os


star2mod = typer.Typer(add_completion=False)

@star2mod.command(no_args_is_help=True)

shahpnmlab

import os
import glob
import pandas as pd
import starfile

# Function to read CSV files
def read_csv_files(directory):
    all_data = []
    for filename in glob.glob(os.path.join(directory, '*.csv')):
        df = pd.read_csv(filename, header=None, names=['X', 'Y', 'Z'])

shahpnmlab

import starfile
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np

# Read the data
warp_apo_df = starfile.read("warp_apo/apoferritin_fsc.star")
pyco_apo_df = starfile.read("pyco_apo/apoferritin_fsc.star")

# Create the plot

shahpnmlab

import napari
import mrcfile

import numpy as np

from pathlib import Path
from magicgui import magicgui
from napari.types import LabelsData, PointsData, ImageData
from scipy.ndimage import distance_transform_edt

shahpnmlab

# Source: https://www.netroby.com/view/3891
yum groupinstall "Development Tools"
yum install ncurses-devel git-core

git clone [email protected]:vim/vim.git

./configure --prefix=/usr --with-features=huge --enable-multibyte --with-python-config-dir=/usr/lib/python2.7/config --enable-pythoninterp=yes
make -j4
make install