In [4]:
%pylab inline
In [5]:
# %run paramtools.ipynb
In [6]:
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import os.path as op
from pprint import pprint as pp
import scipy.stats
import seaborn as sns
import sys
pth = op.abspath("../")
print pth
sys.path.insert(0, pth)
import teigen
import itertools
reload(teigen)
print teigen.__path__
import teigen.tb_vtk
reload (teigen.tb_vtk)
Out[6]:
In [7]:
run_list2 = [
#"compensation method 1 sphere", # callibration
#"compensation method measurement 1 tube", # callibration
### --- evaluation ----
# "compensation method",
# "compensation method 10 spheres",
# "compensation method 3 spheres various radius",
# "compensation method 1 tube", # looks good
# "compensation method N tube", # looks good
# "compensation method 1 tube various radius", # fine
# "compensation method 1 tube various length",# ok
# "compensation method 1 tube mix", # works
# "compensation method 1 cylinder",
# "resolution tube"
# "compensation method 5 tubes", # looks good
# "mix"
# "best test",
# "fixed resolution"
#"generated volume element_number", # asi ok
#
# "mix 2", # test quality of compensation
# "short",
#"element number", # run in the morning
#
# == paper experiments
"generated volume resolution_mm", # done
"generated volume isotropy", # one half
"generated volume radius", # asi ok
#"generated volume length", # do pulky
#"generated volume element_number anisotropic", # asi ok
#"generated volume noise",
]
In [8]:
tg = teigen.tgmain.Teigen()
config = tg.get_default_config()
In [9]:
# pp(config)
config
Out[9]:
In [10]:
tg = teigen.tgmain.Teigen()
In [11]:
if not "configs" in dir():
configs = []
In [ ]:
In [12]:
run_label = "short"
# if run_label in run_list:
for length in [10]:
for rnd in [101, 102, 103]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 3
gc["orientation_anisotropic"] = False
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = 21
config["appearance"]["skip_volume_generation"] = True
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [13]:
run_label = "tube length"
# if run_label in run_list:
for length in [5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48]:
for rnd in [101, 102, 103]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 10
gc["orientation_anisotropic"] = False
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = 20
config["appearance"]["skip_volume_generation"] = True
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [14]:
run_label = "tube length 2"
# if run_label in run_list:
for length in [5, 10, 15, 20, 25, 30, 35, 40, 45]:
for rnd in [101, 102, 103]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 10
gc["orientation_anisotropic"] = False
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = 20
config["appearance"]["skip_volume_generation"] = True
config["output"][run_label_key] = run_label
config["output"][run_label_key] = run_label
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [15]:
run_label = "compensation method"
# if run_label in run_list:
for resolution in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
for rnd in [101]:
for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 10
gc["orientation_anisotropic"] = False
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["radius_distribution_normal"] = False
gc["radius_distribution_mean"] = 20
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 20
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [16]:
run_label = "compensation method 1 sphere"
# if run_label in run_list:
resolutions = [
5, 6, 7, 8,
10, 12, 14, 17, 19,
# 21, 23, 29,
# 30,
# 31, 34, 36, 39,
42, 44, 46, 48,
50, 53, 58, 60,
63, 67,
70, 73, 78,
80, 84, 87,
90, 95
# 100, 150
]
radiuses = [1.]
rnds = [101, 102, 103, 104, 105]
radius_methods = [
"inscribed",
#"circumscribed",
"cylinder surface",
"cylinder volume",
#"average",
"cylinder volume + sphere error",
"cylinder surface + sphere error",
]
for resolution, radius, rnd, radius_method in itertools.product(
resolutions, radiuses, rnds, radius_methods):
# for resolution in [6, 7, 8, 10, 12, 16, 18, 20, 22, 24, 26, 28, 30, 34, 38, 42, 46, 50]:
#for resolution in
# for rnd in [101, 102]:
# for radius_method in [
# ]:
# print("{} {} {} {}".format(resolution, radius, rnd, radius_method))
config = tg.get_default_config()
config["generator_id"] = "Unconnected tubes"
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["orientation_anisotropic"] = False
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 3.0
gc["radius_distribution_minimum"] = 1.0
gc["length_distribution_mean"] = 0.0
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [17]:
run_label = "compensation method 10 spheres"
# if run_label in run_list:
for resolution in [6, 10, 17, 25, 35, 50]:
for rnd in [101]:
for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 10
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = 20
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 0.0
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label]= config
configs.append(config)
In [18]:
run_label = "compensation method 3 spheres various radius"
import itertools
# if run_label in run_list:
resolutions = [25]
for resolution, radius, rnd, radius_method in itertools.product(
[25],
[6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50],
[102, 103],
["inscribed", "cylinder surface", "cylinder volume", "cylinder volume + sphere error"]
):
# for resolution in [25]:
# for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
# for rnd in [102, 103]:
# for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 3
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 0.0
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [19]:
run_label = "compensation method 1 cylinder"
import itertools
# if run_label in run_list:
resolutions = [25]
for resolution, radius, rnd, radius_method in itertools.product(
[10, 15, 20, 25, 35, 50],
[10, 15],
[102, 103],
["inscribed", "cylinder volume", "cylinder surface" ,
"cylinder volume + sphere error", "cylinder surface + sphere error"]
):
# for resolution in [25]:
# for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
# for rnd in [102, 103]:
# for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 3
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 20.0
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["measurement"]["tube_shape"] = False
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [20]:
run_label = "compensation method measurement 1 tube"
import itertools
# if run_label in run_list:
# resolutions = [6, 10, 16, 22, 26, 30, 38, 46, 50]
resolutions = [
5, 7, 9, 11, 13,
# 6, 8, 10, 12, 16, 20, # even numbers
15, 19, 23,
25, 27, 29, 33, 35, 37, 41, 43, 45, 51,
55, 57, 61, 65, 67,
69, 73, 77, 81, 85, 87,
91, 95
]
radiuses = [20.]
rnds = [111, 112, 113, 114]
lengths = [30.]
radius_methods = [
"inscribed",
# "cylinder volume + sphere compensation",
"cylinder surface + sphere error",
# "cylinder surface + sphere error + join error",
"cylinder volume + sphere error",
# "cylinder volume + sphere error + join error"
]
for resolution, radius, rnd, radius_method, length in itertools.product(
resolutions, radiuses, rnds, radius_methods, lengths):
# for resolution in [25]:
# for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
# for rnd in [102, 103]:
# for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["measurement"]["tube_shape"] = True
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [21]:
run_label = "compensation method 1 tube"
import itertools
# if run_label in run_list:
# resolutions = [6, 10, 16, 22, 26, 30, 38, 46, 50]
resolutions = [
21, 25, # 27,
33, 35, #37, 39,
41, 47,
51, 55, #59,
65
]
radiuses = [20.]
rnds = [
# 111, # work fine
11, 12, 13]
lengths = [20., 30., 40.]
radius_methods = [
"inscribed",
#"circumscribed",
# "cylinder surface",
#"cylinder volume",
#"average",
"cylinder volume + sphere error",
"cylinder surface + sphere error",
"cylinder surface + sphere error + join error",
"cylinder volume + sphere error + join error",
]
for resolution, radius, rnd, radius_method, length in itertools.product(
resolutions, radiuses, rnds, radius_methods, lengths):
# for resolution in [25]:
# for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
# for rnd in [102, 103]:
# for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["measurement"]["tube_shape"] = True
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [22]:
run_label = "compensation method N tube"
import itertools
# if run_label in run_list:
# resolutions = [6, 10, 16, 22, 26, 30, 38, 46, 50]
resolutions = [
#21, 22, 25, 27, 33, 35, 37,
39, 41, 45, 51, 55, 59, 65]
radiuses = [20.]
rnds = [
# 111, # work fine
11, 12]
element_numbers = [2, 5]
lengths = [10., 30., 50.]
radius_methods = [
# "inscribed",
#"circumscribed",
# "cylinder surface",
#"cylinder volume",
#"average",
"cylinder volume + sphere error",
"cylinder surface + sphere error",
"cylinder surface + sphere error + join error"
]
for resolution, radius, rnd, radius_method, length, element_number in itertools.product(
resolutions, radiuses, rnds, radius_methods, lengths, element_numbers):
# for resolution in [25]:
# for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
# for rnd in [102, 103]:
# for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = element_number
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 40.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["measurement"]["tube_shape"] = True
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [23]:
run_label = "compensation method 1 tube problem"
# if run_label in run_list:
for resolution in [6, 7, 8, 10, 12, 16, 20, 25, 30, 35, 40, 45, 50]:
for rnd in [101]:
for radius_method in [
#"cylinder surface",
#"cylinder volume",
"cylinder volume + sphere error"
]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = 20
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 20.0
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [24]:
run_label = "compensation method 1 tube various radius"
# if run_label in run_list:
# for resolution in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
for resolution in [25]:
for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
for rnd in [101, 102]:
for radius_method in [
"inscribed",
"cylinder surface",
"cylinder volume",
"cylinder volume + sphere error"
]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 60.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 20.0
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [25]:
run_label = "compensation method 1 tube various length"
# if run_label in run_list:
# for resolution in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
for resolution in [25]:
for length in [20, 30, 40, 45, 50, 55, 60]:
for rnd in [101, 102]:
for radius_method in [
#"cylinder surface", "cylinder volume",
#"cylinder volume + sphere error",
"best"
]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = 10.0
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 60.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 0.1
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [26]:
# 1 tube mix
In [27]:
run_label = "compensation method 1 tube mix"
import itertools
# if run_label in run_list:
resolutions = [25]
for resolution, radius, length, rnd, radius_method in itertools.product(
[25, 35],
[10, 15],
[30, 40, 50],
[102, 103, 104, 105],
[
#"inscribed", "cylinder volume", "cylinder surface" ,
"cylinder volume + sphere error", "cylinder surface + sphere error", "best"]
):
# for resolution in [25]:
# for radius in [6, 7, 8, 10, 12, 16, 20, 25, 30, 40, 50]:
# for rnd in [102, 103]:
# for radius_method in ["inscribed", "circumscribed", "cylinder surface", "cylinder volume", "average"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 1.0
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["measurement"]["tube_shape"] = True
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [28]:
run_label = "compensation method 5 tubes"
# if run_label in run_list:
resolutions = [
# 26, 31, 33, 39,
41, 45, 59]
radiuses = [20., 30.]
rnds = [110]
lengths = [10, 30, 50]
radius_methods = [
# "inscribed",
#"circumscribed",
#"cylinder surface",
#"cylinder volume",
#"average",
"cylinder volume + sphere error",
"cylinder surface + sphere error",
"cylinder surface + sphere error + join error"
]
for resolution, radius, rnd, radius_method, length in itertools.product(
resolutions, radiuses, rnds, radius_methods, lengths):
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 5
gc["radius_distribution_uniform"] = True
gc["radius_distribution_fixed"] = False
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 2.0
gc["radius_distribution_maximum"] = 40.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 2.0
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [29]:
# run_label = "resolution shape"
# if run_label in run_list:
# for resolution in [5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48]:
# for rnd in [101, 102, 103, 104, 105]:
# config = tg.get_default_config()
# config["generator_id"] = 3
# config["output"]["note"] = run_label
# gc = config["generators"]["Unconnected tubes"]
# gc["element_number"] = 10
# gc["orientation_anisotropic"] = False
# gc["length_distribution_mean"] = 0.0
# gc["length_distribution_standard_deviation"] = 0.0
# gc["random_generator_seed"] = rnd
# config["postprocessing"]["measurement_resolution"] = resolution
# config["appearance"]["skip_volume_generation"] = True
# configs.append(config)
run_label = "resolution tube"
# if run_label in run_list:
for resolution in [6, 7, 9, 11, 13, 15, 19, 23, 28, 33, 39, 50]:
for rnd in [102, 103]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 10
gc["orientation_anisotropic"] = False
gc["length_distribution_mean"] = 40.0
gc["length_distribution_standard_deviation"] = 2.0
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = "cylinder volume + sphere error"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [30]:
run_label = "mix"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
45, 53, 57]
element_numbers = [10, 15]
radiuses = [15., 20.]
rnds = [#110,
112]
lengths = [28, 30, 32]
radius_methods = [
#"cylinder surface + sphere error",
"cylinder volume + sphere error",
# "cylinder volume + sphere error + man", # fine
# "cylinder surface + sphere error + join error", # fine
# "cylinder surface + sphere error + join error man" # fine
]
for resolution, radius, rnd, radius_method, length, element_number in itertools.product(
resolutions, radiuses, rnds, radius_methods, lengths, element_numbers):
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = element_number
gc["radius_distribution_uniform"] = True
gc["radius_distribution_fixed"] = False
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 10.0
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [31]:
run_label = "mix 2"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
45,
# 51, ok kromě cylinder surface + sphere error
53,
55]
element_numbers = [10]
radiuses = [15., 20.]
rnds = [110,
112,
113,
]
lengths = [28, 30, 32]
radius_methods = [
# "inscribed",
"cylinder surface + sphere error",
"cylinder volume + sphere error",
"cylinder surface + sphere error + join error", # fine
"cylinder volume + sphere error + join error", # fine
# "cylinder volume + sphere error + man", # fine
# "cylinder surface + sphere error + join error man" # fine
]
for resolution, radius, rnd, radius_method, length, element_number in itertools.product(
resolutions, radiuses, rnds, radius_methods, lengths, element_numbers):
config = tg.get_default_config()
config["generator_id"] = "Unconnected tubes"
config["output"]["note"] = run_label + " " + radius_method
config["areasampling"]["voxelsize_mm"] = [1.0, 1.0, 1.0]
config["areasampling"]["areasize_mm"] = [100.0, 100.0, 100.0]
config["areasampling"]["areasize_px"] = [100, 100, 100]
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = element_number
gc["radius_distribution_uniform"] = True
gc["radius_distribution_fixed"] = False
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = radius
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = length
gc["length_distribution_standard_deviation"] = 10.0
gc["random_generator_seed"] = rnd
gc['radius_distribution_uniform'] = False
gc['radius_distribution_normal'] = True
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [ ]:
In [32]:
run_label = "best test"
# if run_label in run_list:
for resolution in [25, 30, 35]:
for rnd in [106, 107, 108, 109, 110]:
for radius_method in ["best"]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 1
gc["radius_distribution_uniform"] = True
gc["radius_distribution_fixed"] = False
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = 10
gc["radius_distribution_standard_deviation"] = 2.0
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 30.0
gc["length_distribution_standard_deviation"] = 10.0
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [33]:
run_label = "fixed resolution"
# if run_label in run_list:
for resolution in [25]:
for rnd in [106, 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119]:
for radius_method in [
# "inscribed",
# "average",
#"cylinder volume + sphere error",
#"cylinder surface + sphere error",
"best",
]:
config = tg.get_default_config()
config["generator_id"] = 3
config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 5
gc["radius_distribution_uniform"] = True
gc["radius_distribution_fixed"] = False
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = 10
gc["radius_distribution_standard_deviation"] = 2.0
gc["radius_distribution_maximum"] = 30.0
gc["radius_distribution_minimum"] = 3.0
gc["length_distribution_mean"] = 30.0
gc["length_distribution_standard_deviation"] = 2.0
gc["random_generator_seed"] = rnd
config["postprocessing"]["measurement_resolution"] = resolution
config["appearance"]["skip_volume_generation"] = True
config["measurement"]["polygon_radius_selection_method"] = radius_method
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [34]:
## Paper figures
def get_paper_config(resolution_mm=0.02):
config = tg.get_default_config()
config["generator_id"] = 3
#config["output"]["note"] = run_label + " " + radius_method
gc = config["generators"]["Unconnected tubes"]
gc["element_number"] = 30
gc["radius_distribution_uniform"] = True
gc["radius_distribution_fixed"] = False
gc["orientation_anisotropic"] = False
gc["radius_distribution_mean"] = 0.2
gc["radius_distribution_standard_deviation"] = 0.1
gc["radius_distribution_maximum"] = 3.0
gc["radius_distribution_minimum"] = .3
gc['radius_distribution_uniform'] = False
gc['radius_distribution_normal'] = True
gc["length_distribution_mean"] = 3.0
gc["length_distribution_standard_deviation"] = .1
gc["volume_fraction"] = 0.5
gc["random_generator_seed"] = 100
gc["orientation_anisotropic"] = False
config["postprocessing"]["gaussian_blur"] = True
config["postprocessing"]["gaussian_filter_sigma_mm"] = 0.04
config["postprocessing"]["measurement_resolution"] = 35
config["postprocessing"]['add_noise'] = False
config["appearance"]["skip_volume_generation"] = False
config["measurement"]["polygon_radius_selection_method"] = "inscribed"
config['areasampling']["areasize_mm"] = [10.0, 10.0, 10.0]
config['areasampling']["areasize_px"] = [10.0/resolution_mm, 10.0/resolution_mm, 10.0/resolution_mm]
config['areasampling']["voxelsize_mm"] = [resolution_mm, resolution_mm, resolution_mm]
config["output"][run_label_key] = run_label
# config['filepattern'] = "~/teigen_data/generated_resolution_mm_{seriesn:03d}/data{:06d}.jpg"
return config
In [35]:
# bez šumu
run_label = "generated volume resolution_mm"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [.5, .4, .3, .2, 0.1, 0.08, 0.06, 0.04, 0.02, .01]
element_numbers = [30]
radiuses = [.2]
rnds = [
110,
# 111,
# 112
]
lengths = [3.0]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for resolution_mm, radius_method in itertools.product(
resolutions_mm, radius_methods):
config = get_paper_config(resolution_mm=resolution_mm)
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
config['filepattern'] = "~/teigen_data/teigen_resolution_mm_" + str(resolution_mm) + "_{seriesn:03d}/data{:06d}.jpg"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [36]:
# bez šumu
run_label = "generated volume isotropy"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [
#.5, .4, .3, .2, 0.1, 0.08, 0.06,
0.04, 0.02, .01]
#0.4, 0.2, .1
isotropy_values = [
5, 4, 3, 2, 1, 0.8, 0.6, 0.3, 0.2, .1
]
element_numbers = [30]
radiuses = [.2]
rnds = [
110,
# 111,
# 112
]
lengths = [3.0]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for isotropy, radius_method in itertools.product(
isotropy_values, radius_methods):
config = get_paper_config()
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
gc["orientation_anisotropic"] = True
gc["orientation_variance_rad"] = isotropy
config['filepattern'] = "~/teigen_data/teigen_isotropy_" + str(isotropy) + "_{seriesn:03d}/data{:06d}.jpg"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [37]:
run_label = "generated volume element_number"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [.2]
element_numbers = [20, 30, 40, 50, 60, 70, 80, 90, 100, 110]
radiuses = [.5]
rnds = [
110,
# 111,
# 112
]
lengths = [3.0]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for element_number, radius_method in itertools.product(
element_numbers, radius_methods):
config = get_paper_config()
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
gc["element_number"] = element_number
config['filepattern'] = "~/teigen_data/teigen_element_number_" + str(element_number) + "_{seriesn:03d}/data{:06d}.jpg"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [38]:
run_label = "generated volume element_number anisotropic"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [.2]
element_numbers = [20, 30, 40, 50, 60, 70, 80, 90, 100, 110]
radiuses = [.5]
rnds = [
110,
# 111,
# 112
]
lengths = [3.0]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for element_number, radius_method in itertools.product(
element_numbers, radius_methods):
config = get_paper_config()
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
gc["element_number"] = element_number
gc["orientation_anisotropic"] = True
gc["maximum_1000_iteration_number"] = 30
config['filepattern'] = "~/teigen_data/teigen_element_number_anisotropic_" + str(element_number) + "_{seriesn:03d}/data{:06d}.jpg"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [39]:
run_label = "generated volume radius"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [.02]
element_numbers = [30]
radiuses = [0.06, 0.08, 0.1, 0.2, .3, .5, .8, 1.0, 1.5, 3.0]
rnds = [
110,
# 111,
# 112
]
lengths = [3.0]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for radius, radius_method in itertools.product(
radiuses, radius_methods):
config = get_paper_config()
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
gc["radius_distribution_mean"] = radius
gc["radius_distribution_uniform"] = False
gc["radius_distribution_fixed"] = True
gc["radius_distribution_normal"] = False
config['filepattern'] = "~/teigen_data/teigen_radius_" + str(radius) + "_{seriesn:03d}/data{:06d}.jpg"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [40]:
run_label = "generated volume length"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [.02]
element_numbers = [30]
radiuses = [0.2]
rnds = [
110,
# 111,
# 112
]
lengths = [
# 0.05, 0.1, 0.2,
0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4.0,
#5.0, 6.0
]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for radius_method, length in itertools.product(
radius_methods, lengths):
config = get_paper_config()
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
# gc["radius_distribution_mean"] = radius
gc["length_distribution_mean"] = length
config['filepattern'] = "~/teigen_data/teigen_length_" + str(length) + "_{seriesn:03d}/data{:06d}.jpg"
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [41]:
run_label = "generated volume noise"
# if run_label in run_list:
# if run_label in run_list:
# for resolution in [25, 30, 35]:
# for rnd in [106, 107, 108, 109, 110]:
# for radius_method in ["best"]:
resolutions = [
# 26, 31, 33, 39,
# 41, 45, 59,
# 47,
# 15,
# 25,
35,
# 45,
# 55,
# 65,
# 51, ok kromě cylinder surface + sphere error
#53,
#55
]
resolutions_mm = [.02]
element_numbers = [30]
radiuses = [.3, .5, .8, 1.1, 1.5]
rnds = [
#110,
111,
# 112
]
noises = [20, 40, 60, 80, 100, 120, 140, 160, 200, 220]
lengths = [3.0]
radius_methods = [
"inscribed",
# "cylinder surface + sphere error",
# "cylinder volume + sphere error",
# "cylinder surface + sphere error + join error",
# "cylinder volume + sphere error + join error",
]
for noise, radius_method in itertools.product( noises, radius_methods):
config = get_paper_config()
gc = config["generators"]["Unconnected tubes"]
config["output"]["note"] = run_label + " " + radius_method
config['filepattern'] = "~/teigen_data/teigen_noise_" + str(noise) + "_{seriesn:03d}/data{:06d}.jpg"
config["postprocessing"]['add_noise'] = True
config["postprocessing"]['noise_exponent'] = 0.
config["postprocessing"]['noise_std'] = noise
config["postprocessing"]['noise_mean'] = 0.
config["postprocessing"]['noise_lambda0'] = 0.02
config["postprocessing"]['noise_lambda1'] = 1.00
config["output"][run_label_key] = run_label
# configs[run_label] = config
configs.append(config)
In [42]:
In [43]:
#import psutil
#def print_number_of_opened_files():
# for proc in psutil.process_iter():
# print proc.open_files()
In [44]:
# run_configs(configs)
In [1]:
config