stephanmg

import numpy as np
import pandas as pd
from pypesto.store import read_from_hdf5
import os
import matplotlib.pyplot as plt
from matplotlib import cm
from more_itertools import unique_everseen
from pathlib import Path
import argparse
from pypesto.visualize import optimizer_convergence

stephanmg

     DATASET "x_names" {
         DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_UTF8;
            CTYPE H5T_C_S1;
         }
         DATASPACE  SIMPLE { ( 71 ) / ( 71 ) }
         DATA {
         (0): "init_Cells", "init_Cells_Cycle_G2_rel",

stephanmg

def run_optimization(importer, optimizer, output_folder, yaml_file, algorithm_name, num_starts, parallel):
    """
    Run the optimization
    Parameters
    ----------
    importer:
        PEtab model importer
    optimizer:
        name of the optimizer
    output_folder:

stephanmg

# Amici.py

def check_gradients(self, x: np.ndarray = None, *args, **kwargs):
       if x is None and 'petab_problem' in dir(self.amici_object_builder):
           x = self.amici_object_builder.petab_problem.x_nominal_scaled
           x_free = self.amici_object_builder.petab_problem.x_free_indices
       return ObjectiveBase.check_gradients(self, x=x, x_free=x_free, *args, **kwargs)
       
       
# Base.py

stephanmg

parpool(4)

parfor K = 1 : 4
  if K == 1; compute_function_val(10); end
  if K == 2; compute_function_val(20); end
  if K == 3; compute_function_val(30); end
  if K == 4; compute_function_val(40); end
end

function y=compute_function_val(m) 

stephanmg

GameObject cone = GameObject.Find("cone");
Mesh mesh = cone.GetComponent<MeshFilter>().sharedMesh;
AssetDatabase.CreateAsset(msh, assetpath);
PrefabUtility.SaveAsPrefabAsset(mesh, prefabpath);
AssetDatabase.SaveAssets();
AssetDatabase.Refresh();

stephanmg

using UnityEngine;
using UnityEditor;
using System.Collections;
 
// an Editor method to create a cone primitive (so far no end caps)
// the top center is placed at (0/0/0)
// the bottom center is placed at (0/0/length)
// if either one of the radii is 0, the result will be a cone, otherwise a truncated cone
// note you will get inevitable breaks in the smooth shading at cone tips
// note the resulting mesh will be created as an asset in Assets/Editor

stephanmg

using UnityEngine;
using System.Collections;

[RequireComponent (typeof (MeshFilter))]
public class Cone : MonoBehaviour {
	
	/// subdivision
	public int subdivisions = 10;
	/// height and radius
	public float radius = 1f;

stephanmg

#!/bin/bash

# number of neurons
numNeurons=100

# get neurons
for index in $(seq 1 "$numNeurons"); do
  python get_swc.py --search "brain_region=neocortex" \
                     --filter "cell_type=pyramidal" \
                     --filter "archive=Hrvoj-Mihic_Semendeferi" \

stephanmg

param(
[Parameter(Mandatory=$true)][String]$APPVEYOR_TOKEN="",
[Parameter(Mandatory=$true)][String]$PROJECT_SLUG="",
[String]$APPVEYOR_USER=stephanmg)

if ([string]::IsNullOrWhiteSpace($APPVEYOR_TOKEN)) { "No AppVeyor API token given" }
if ([string]::IsNullOrWhiteSpace($PROJECT_SLUG)) { "No project slug to trigger given" }
if ([string]::IsNullOrWhiteSpace($APPVEYOR_USER)) { "No Appveyor user given }

$headers = @{Authorization = "Bearer $APPVEYOR_TOKEN" }