ericspod

Code is clean if it can be understood easily – by everyone on the team. Clean code can be read and enhanced by a developer other than its original author. With understandability comes readability, changeability, extensibility and maintainability.

---

General rules

1. Follow standard conventions.
2. Keep it simple stupid. Simpler is always better. Reduce complexity as much as possible.
3. Boy scout rule. Leave the campground cleaner than you found it.
4. Always find root cause. Always look for the root cause of a problem.

Design rules

ericspod

import os
import sys
import json
import datetime
from typing import Union

# from https://gist.github.com/jannismain/e96666ca4f059c3e5bc28abb711b5c92


class CompactJSONEncoder(json.JSONEncoder):

ericspod

from ignite.engine import Events, Engine

class Attachable:
    """
    This class contains an internal dictionary `attach_map` associating events with the bound methods to be triggered
    on those events. This dictionary can be populated by the contructor or by external clients after construction and 
    before `attach` is called. 
    """
    def __init__(self, attach_map):
        self.attach_map = dict(attach_map)

ericspod

import torch
import warnings
import threading
import numpy as np

from ignite.engine.engine import Engine, Events

def ensure_tuple(vals):
    """
    Returns a tuple containing just `vals` if it is not a list or tuple, or `vals` converted to a tuple otherwise.

ericspod

def matZero(n,m):
    '''Return a list of lists with the given dimensions containing zeros.'''
    return [[0]*m for i in range(n)]


def matIdent(n):
    '''Return a list of lists defining the identity matrix of rank `n'.'''
    mat=matZero(n,n)
    for nn in range(n):
        mat[nn][nn]=1.0

ericspod

import vtk
import os,sys,math

# read unstructured grid
r=vtk.vtkXMLUnstructuredGridReader()
r.SetFileName(sys.argv[1]) # first command line argument after script name
r.Update()

orig=r.GetOutput()

ericspod

from eidolon import *


# The Catmull-Rom basis types assume a fixed set of control points: 4 for 1D, 4**2 for 2D, and 4**3 for 3D. 
# The piecewise Catmull-Rom allows a definition with an arbitrarily sized lattice of control points which is 
# then divided up into individual elements which share control points of neighbours. The line example in the
# wiki shows an element composed of 3 lines. To allow the configuration of the element type, the basis function
# which returns coefficients for piecewise Catmull-Rom accepts extra parameters in addition to the xi coordinates
# (u,v,w): `ul', `vl', `wl' stating the dimensions of the control point lattice, `limits' stating for each dimension if 

ericspod

# Copy this function into the Eidolon console then you can call it as described below.
def cropImage(img,minz,maxz,mint,maxt):
    '''Crop image `img' in the Z (minz to maxz) and T dimensions (mint to maxt).'''
    arr=img.plugin.getImageObjectArray(img) # break the image down into spatial components and numpy array
    arr['array']=arr['array'][:,:,minz:maxz,mint:maxt] # crop the numpy array
    arr['pos']=img.images[img.getVolumeStacks()[0][minz]].position # set the position to the bottom of the new stack
    newimg=img.plugin.createObjectFromArray(img.getName()+'Crop',**arr) # create new image object
    mgr.addSceneObject(newimg) # add image to scene
    return newimg # return image