Alex Liberzon alexlib

## basic_3d_point_picker.py
from pathlib import Path

import mrcfile
import napari
import numpy as np
from magicgui import magicgui

OUTPUT_DIRECTORY = 'picking'
Path(OUTPUT_DIRECTORY).mkdir(exist_ok=True, parents=True)

## viewer.py
from pathlib import Path
from typing import Dict
from enum import Enum

import napari
import numpy as np
import mrcfile
import pandas as pd
import starfile
import eulerangles

## tomo_vis_napari_demo.py
import numpy as np
import mrcfile
import starfile
from eulerangles import euler2matrix, invert_rotation_matrices
import napari
from fuzzywuzzy import fuzz, process

# Read in data
particle_file = 'particles_10.00Apx.star'
volume_file = 'TS_01.mrc_10.00Apx.mrc'

## gist:47c0abcc6e0840a939e81c486b89273c

      
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                alexlib
                / gist:47c0abcc6e0840a939e81c486b89273c
            
            
              Last active
              April 23, 2022 15:53
            
              
                installation of OpenPTV + PyPTV on headless VNC server based on Ubuntu 20.04 and Xfce 
              
          
    Use Docker image

    docker run -d -p 25901:5901 -p 26901:6901 accetto/ubuntu-vnc-xfce-chromium-g3:latest

access headless server (note the password is also headless, unless you change it)

http://localhost:26901/vnc_lite.html?password=headless
Open Terminal and run these commands:


## _installation_paches.md

      
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                alexlib
                / _installation_paches.md
            
            
              Last active
              April 24, 2022 06:09
            
              
                Bug tracking of OpenPTV + PyPTV on Windows 10 with Python 3.10
              
          
    Recreating the bug reported in the forum

https://groups.google.com/d/msgid/openptv/43837409-aac5-407c-a8bf-37e96a95f599n%40googlegroups.com?utm_medium=email&utm_source=footer
Installation procedure:

conda create -n pyptv_py310win python=3.10 -y
conda activate pyptv_py310win
python -m pip install --upgrade pip
pip install numpy
pip install pyptv --index-url https://pypi.fury.io/pyptv --extra-index-url https://pypi.org/simple


## github_actions.yaml
name: CI

on:
  push:
    branches:
    - main
  pull_request:
    branches:
    - main

## conda-pack-win.md

      
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                alexlib
                / conda-pack-win.md
            
            
              Created
              April 19, 2022 07:45
                — forked from pmbaumgartner/conda-pack-win.md
            
              
                Conda-Pack Windows Instructions
              
          
    Packing Conda Environments

You must be using conda for this approach. You will need conda installed on the Source machine and the Target machine. The Source machine must have an internet connection, the Target does not. The OS in both environments must match; no going from macOS to Win10 for example.
1. (Source) Install conda-pack in your base python environment.
conda install -c conda-forge conda-pack


## create_6_points_file.ipynb

      
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                alexlib
                / create_6_points_file.ipynb
            
            
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              April 17, 2022 22:16
            
              
                Visualize a 3d cloud of points from a file and then click on a 2D image projection of those points with visualizing the clicks using text in Matplotlib and Jupyter 
              
          
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## create_enable_binary_wheel.sh
git clone https://github.com/enthought/enable
sudo apt-get update
sudo apt-get install libx11-dev
sudo apt-get install libglu1-mesa-dev
sudo apt-get install swig3.0
sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
conda create -n enable python=3.8 -y
conda activate enable
sudo apt install g++
pip install cython

## moving_average.py
import numpy as np

def moving_average(a, n=5) :
    """ creates moving average along the first axis of the
    three dimensional numpy array, aka stack of images
    """
    ret = np.cumsum(a, dtype=float, axis=0)
    ret[n:,:,:] = ret[n:,:,:] - ret[:-n,:,:]
    return ret[n - 1:,:,:] / n
	from pathlib import Path

	import mrcfile
	import napari
	import numpy as np
	from magicgui import magicgui

	OUTPUT_DIRECTORY = 'picking'
	Path(OUTPUT_DIRECTORY).mkdir(exist_ok=True, parents=True)
	from pathlib import Path
	from typing import Dict
	from enum import Enum

	import napari
	import numpy as np
	import mrcfile
	import pandas as pd
	import starfile
	import eulerangles
	git clone https://github.com/enthought/enable
	sudo apt-get update
	sudo apt-get install libx11-dev
	sudo apt-get install libglu1-mesa-dev
	sudo apt-get install swig3.0
	sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
	conda create -n enable python=3.8 -y
	conda activate enable
	sudo apt install g++
	pip install cython
	import numpy as np

	def moving_average(a, n=5) :
	""" creates moving average along the first axis of the
	three dimensional numpy array, aka stack of images
	"""
	ret = np.cumsum(a, dtype=float, axis=0)
	ret[n:,:,:] = ret[n:,:,:] - ret[:-n,:,:]
	return ret[n - 1:,:,:] / n