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test_ami_graph.py
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"""
tests AmiGraph, AmiNode, AmiEdge, AmiIsland
"""
from skimage import io
import cv2
import logging
import unittest
from collections import Counter
# library
from pathlib import PurePath
import matplotlib.pyplot as plt
import networkx as nx
import numpy
import numpy as np
import pytest
from skimage import data, morphology
from skimage.measure import approximate_polygon, subdivide_polygon
from skimage.morphology import skeletonize
# local
import context
from pyamiimage.ami_edge_manager import AmiEdgeAnalyzer, X, Y
from pyamiimage.ami_graph_all import AmiNode, AmiIsland, AmiGraph, AmiEdge
from pyamiimage.ami_image import AmiImage
from pyamiimage.ami_plot import AmiEdgeTool, AmiLine
from pyamiimage.ami_util import AmiUtil
from pyamiimage.bbox import BBox
from pyamiimage.text_box import TextBox, TextUtil
from resources import Resources
logger = logging.getLogger(__name__)
interactive = False
RAW = 0
BOXED = 1
ARROWS_1 = "arrows1"
class TestAmiGraph:
def setup_class(self):
"""
resources are created once only in self.resources.create_ami_graph_objects()
Make sure you don't corrupt them
we may need to add a copy() method
:return:
"""
self.resources = Resources()
self.resources.create_ami_graph_objects()
def setup_method(self, method):
#
self.arrows1 = self.resources.arrows1_image_file
self.nx_graph_arrows1 = self.resources.nx_graph_arrows1
self.biosynth1_binary = self.resources.biosynth1_binary
self.biosynth1_elem = self.resources.biosynth1_elem
self.nx_graph_biosynth3 = self.resources.biosynth3_dto.nx_graph
self.nx_graph_prisma = self.resources.nx_graph_prisma
self.battery1_image = self.resources.battery1_image
self.nx_graph_battery1 = self.resources.nx_graph_battery1
# return self
@unittest.skip("exploration")
def test_sknw_5_islands(self):
"""
This checks all the fields that sknw returns
also explares many primitives in nx.graph
:return:
"""
skel_path = Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
assert isinstance(skel_path, PurePath)
skeleton_array = AmiImage.create_white_skeleton_from_file(skel_path)
AmiUtil.check_type_and_existence(skeleton_array, np.ndarray)
# nx_graph = AmiGraph.create_nx_graph_from_skeleton(skeleton_array)
# nx_graph = AmiGraph.create_nx_graph_from_arbitrary_image_file(R esources.BIOSYNTH1_CROPPED_ARROWS_RAW)
nx_graph = self.resources.arrows1_nx_graph
AmiUtil.check_type_and_existence(nx_graph, nx.classes.multigraph.MultiGraph)
assert list(nx_graph.nodes) == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26]
# this fails because it's a NodeView
# assert nx_graph.nodes() == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
# 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]
print(f"nodes {type(nx_graph.nodes)} {nx_graph.nodes()}")
# print (f"edges {nx_graph.edges()}")
assert list(nx_graph.edges) == [
(0, 2, 0), (1, 4, 0), (2, 4, 0), (2, 3, 0), (2, 7, 0), (4, 5, 0), (4, 6, 0), (8, 19, 0),
(9, 19, 0), (10, 12, 0), (11, 13, 0), (12, 13, 0), (12, 18, 0), (13, 14, 0), (13, 15, 0),
(16, 18, 0), (17, 18, 0), (18, 20, 0), (19, 26, 0), (21, 24, 0), (22, 24, 0), (23, 24, 0),
(24, 25, 0)], f"edges {list(nx_graph.edges)}"
# np.testing.assert_array_equal(x, y, msg)
# AmiUtil.check_type_and_existence(nx_graph.nodes, nx.classes.reportviews.NodeView)
#
# AmiUtil.check_type_and_existence(nx_graph.edges, nx.classes.reportviews.MultiEdgeView)
node1ps = nx_graph.nodes[1][AmiNode.CENTROID]
assert str(node1ps) == "[ 83 680]"
edge_yx = nx_graph.edges[(0, 2, 0)][AmiEdge.PTS]
edge_xy = np.flip(edge_yx, 1)
expected = np.array(
[[844, 82], [845, 83], [846, 84], [847, 84], [848, 85], [849, 85], [850, 86], [851, 86],
[852, 87], [853, 87], [854, 87], [855, 88], [856, 89], [857, 91]], dtype=np.int16)
# print(f"expected {type(expected)} {expected}")
# can't get this to work
# assert np.testing.assert_array_equal(edge_xy, expected) #, err_msg=f"found {edge_xy}")
# but this does
assert np.array_equal(edge_xy, expected), f"found {edge_xy}"
def test_ami_edges(self):
"""
wrappers for nx_graph
"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.BIOSYNTH1_CROPPED_ARROWS_RAW)
# ami_graph = self.resources.arrows1_ami_graph
dto = Resources.get_image_dto(Resources.BIOSYNTH1_CROPPED_ARROWS_RAW,
raw_image_shape=(315, 1512)
)
ami_graph = dto.ami_graph
# ami_graph = Resources.create_graph(ARROWS_1)
print("------------------")
ami_edges = ami_graph.get_or_create_all_ami_edges()
assert len(ami_edges) == 23, f"found {len(ami_edges)}"
# @unittest.skip("needs multigraph adding NYI")
def test_segmented_edges(self):
"""
analyse 4 arrows and convert to lines
Note:
nx_graph[i][j]["pts"] seens to be the same as nx_graph[j][i]["pts"]
NO! there are 2 edges in opposite directions
Note: double backslash is an escape, not meaningful
:return:
"""
# nx_graph = AmiGraph.create_nx_graph_from_arbitrary_image_file(Resources.BIOSYNTH1_CROPPED_ARROWS_RAW)
nx_graph = self.resources.nx_graph_arrows1
assert nx_graph is not None, f"nx_graph is not none"
"""
{0, 1, 2, 3, 4, 5, 6, 7}, # double arrow
0 6
/ \\
3----2-------------4----5
\\ /
7 1
[(0, 2), (1, 4), (2, 4), (2, 3), (2, 7), (4, 5), (4, 6),
"""
print("\n2 0", nx_graph[2][0][0][AmiEdge.PTS][:2:-2])
points0_2 = nx_graph[2][0][0][AmiEdge.PTS]
expected_numpy = np.array([[82, 844],
[83, 845],
[84, 846],
[84, 847],
[85, 848],
[85, 849],
[86, 850],
[86, 851],
[87, 852],
[87, 853],
[87, 854],
[88, 855],
[89, 856],
[91, 857]])
assert type(expected_numpy[0]) is np.ndarray
assert type(expected_numpy[0][0]) is np.int64
assert np.array_equal(points0_2, expected_numpy), f"found {points0_2}"
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.BIOSYNTH1_CROPPED_ARROWS_RAW)
ami_graph = self.resources.arrows1_ami_graph
ami_edges = ami_graph.get_or_create_all_ami_edges()
assert len(ami_edges) == 23
for ami_edge in ami_edges:
for tol in range(1, 10, 3):
segments = ami_edge.create_line_segments(tolerance=tol)
print(f"tol {tol} edge {ami_edge.start_id, ami_edge.end_id} segments {len(segments)} -> {segments}")
"""
{8, 9, 26, 19}, # y-shaped arrow-less
(8, 19), (9, 19), (19, 26),
8 26
| |
----19-----
|
26
"""
"""
{10, 11, 12, 13, 14, 15, 16, 17, 18, 20}, # bifurcated arrow
(10, 12), (11, 13), (12, 13), (12, 18), (13, 14), (13, 15), (16, 18), (17, 18), (18, 20),
"""
"""
{21, 22, 23, 24, 25}] # simple arrow
(21, 24), (22, 24), (23, 24), (24, 25)]
21
|
|
|
22 | 23
\\ | /
\\ | /
24
|
|
25
"""
return
@unittest.skip("no actiom")
def test_arrows(self):
"""
looks for arrowheads, three types
* point with shaft and two edges going "backwards" symmetrically
* point with shaft, 2 edges backward and short one forward (result of thinning filled triangle)
* half arrow. point with one edge backwards (e.g. in chemical equilibrium
:return:
"""
AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.BIOSYNTH1_CROPPED_ARROWS_RAW, reader=Resources.IMAGE_METHOD)
def test_islands(self):
"""
Create island_node_id_sets using sknw/NetworkX and check basic properties
:return:
"""
# nx_graph = AmiGraph.create_nx_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
nx_graph = self.resources.nx_graph_arrows1
connected_components = list(nx.algorithms.components.connected_components(nx_graph))
assert nx.algorithms.components.number_connected_components(nx_graph) == 4
connected_components = list(nx.algorithms.components.connected_components(nx_graph))
assert type(connected_components) is list, f"type of connected components should be list"
assert connected_components == [
{0, 1, 2, 3, 4, 5, 6, 7},
{8, 9, 26, 19},
{10, 11, 12, 13, 14, 15, 16, 17, 18, 20},
{21, 22, 23, 24, 25},
]
assert type(connected_components[0]) is set and len(connected_components[0]) == 8, \
f"components should be sets and first len == 8"
assert type(list(connected_components[0])[0]) is int, f"members should be int"
ami_graph = AmiGraph(nx_graph)
ami_graph.read_nx_graph(nx_graph)
island_node_id_sets = ami_graph.get_or_create_ami_islands()
assert len(island_node_id_sets) == 4
assert type(island_node_id_sets[0]) is AmiIsland
assert island_node_id_sets[0].node_ids == {0, 1, 2, 3, 4, 5, 6, 7}
def test_node_centroid(self):
"""
Tests
:return:
"""
ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.BIOSYNTH1_CROPPED_ARROWS_RAW)
xy = ami_graph.get_or_create_centroid_xy(0)
assert xy == [844.0, 82.0]
def test_get_nx_edge_list_for_node(self):
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
edges = ami_graph.get_nx_edge_list_for_node(24)
assert edges == [(24, 21, 0), (24, 22, 0), (24, 23, 0), (24, 25, 0)], \
f"found {edges} expected {[(24, 21, 0), (24, 22, 0), (24, 23, 0), (24, 25, 0)]}"
def test_get_nx_edge_lengths_for_node(self):
# ami_graph = self.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
lengths = ami_graph.get_nx_edge_lengths_by_edge_list_for_node(24)
print(f"lengths {lengths}")
lengthsx = [length for length in lengths.values()]
assert [0.1 + 0.2, 0.2 + 0.4] == pytest.approx([0.3, 0.6])
aaa = [30.00, 8.944, 9.848, 12.041]
expect = pytest.approx(aaa, 0.001)
assert lengthsx == expect, f"found {lengthsx} expected {expect}"
def test_get_nodes_with_degree(self):
"""
uses get_nodes_with_degree on each node to create lists
:return:
"""
# ami_graph = self.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
self.assert_degrees(ami_graph, 4, [2, 4, 13, 18, 24])
self.assert_degrees(ami_graph, 3, [12, 19])
self.assert_degrees(ami_graph, 2, [])
self.assert_degrees(ami_graph, 1, [0, 1, 3, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26])
def test_distal_node(self):
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
edge = ami_graph.get_nx_edge_list_for_node(1)[0]
ami_edge0 = ami_graph.get_or_create_ami_edge_from_ids(edge[0], edge[1], edge[2])
assert ami_edge0.start_id == 1
assert ami_edge0.remote_node_id(1) == 4
assert ami_edge0.remote_node_id(4) == 1
assert ami_edge0.remote_node_id(None) is None
assert ami_edge0.remote_node_id(3) is None
def test_get_neighbours(self):
# ami_graph = self.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
assert [2] == ami_graph.get_or_create_ami_node(0).get_neighbour_ids()
assert [4] == ami_graph.get_or_create_ami_node(1).get_neighbour_ids()
assert [0, 4, 3, 7] == ami_graph.get_or_create_ami_node(2).get_neighbour_ids()
assert [10, 13, 18] == ami_graph.get_or_create_ami_node(12).get_neighbour_ids()
@classmethod
def create_ami_graph_from_arbitrary_image_file(cls, path):
"""
creates nx_graph and wraps it in AmiGraph object
:return: AmiGraph
"""
nx_graph = AmiGraph.create_nx_graph_from_arbitrary_image_file(path)
ami_graph = AmiGraph(nx_graph=nx_graph)
return ami_graph
def test_get_angles_of_edges_node(self):
# ami_graph = self.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
edge_ids = ami_graph.get_nx_edge_list_for_node(24)
assert edge_ids == [(24, 21, 0), (24, 22, 0), (24, 23, 0), (24, 25, 0)]
angles = []
for i, edgei_id in enumerate(edge_ids):
edgei = ami_graph.get_ami_edge_from_nx_id(edgei_id)
for j, edgej_id in enumerate(edge_ids):
if j > i:
edgej = ami_graph.get_ami_edge_from_nx_id(edgej_id)
common_node_id = AmiEdge.get_common_node_id(edgei_id, edgej_id)
if common_node_id is not None:
print(f"{edgei_id} {edgej_id} common_node {common_node_id}")
angle_i_j = ami_graph.get_angle_between_nodes(
edgei.remote_node_id(common_node_id),
common_node_id,
edgej.remote_node_id(common_node_id),
)
angleicj = (i, common_node_id, j, round(angle_i_j, 3))
angles.append(angleicj)
assert angles == [
(0, 24, 1, -1.107),
(0, 24, 2, 1.153),
(0, 24, 3, 3.058),
(1, 24, 2, 2.26),
(1, 24, 3, -2.118),
(2, 24, 3, 1.906),
]
def test_bboxes(self):
"""
Create bounding boxes for islands
:return:
"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
islands = ami_graph.get_or_create_ami_islands()
assert len(islands) == 4, "arrows"
bbox_list = []
for island in islands:
bbox = island.get_or_create_bbox()
assert type(bbox) is BBox
bbox_list.append(bbox)
assert len(bbox_list) == 4
# this is horrible and fragile, need __eq__ for bbox
assert str(bbox_list[0]) == "[[661, 863], [82, 102]]", f"bbox_list[0] is {bbox_list[0]}"
def test_line_segments(self, interact=interactive):
"""
split edges into segments (Douglas-Paucker) - Python tutorial
:return:
"""
interactive = False
ignore_hand = True
fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=(9, 4))
if not ignore_hand:
hand = np.array(
[
[1.64516129, 1.16145833],
[1.64516129, 1.59375],
[1.35080645, 1.921875],
[1.375, 2.18229167],
[1.68548387, 1.9375],
[1.60887097, 2.55208333],
[1.68548387, 2.69791667],
[1.76209677, 2.56770833],
[1.83064516, 1.97395833],
[1.89516129, 2.75],
[1.9516129, 2.84895833],
[2.01209677, 2.76041667],
[1.99193548, 1.99479167],
[2.11290323, 2.63020833],
[2.2016129, 2.734375],
[2.25403226, 2.60416667],
[2.14919355, 1.953125],
[2.30645161, 2.36979167],
[2.39112903, 2.36979167],
[2.41532258, 2.1875],
[2.1733871, 1.703125],
[2.07782258, 1.16666667],
]
)
# subdivide polygon using 2nd degree B-Splines (green)
new_hand = hand.copy()
ncycle = 5 # doubles the number of points/splines each cycle
for _ in range(ncycle):
new_hand = subdivide_polygon(new_hand, degree=2, preserve_ends=True)
# approximate subdivided polygon with Douglas-Peucker algorithm (orange line)
tolerance = 0.02
appr_hand = approximate_polygon(new_hand, tolerance=tolerance)
ax1.plot(hand[:, 0], hand[:, 1])
ax1.plot(appr_hand[:, 0], appr_hand[:, 1])
points = np.array(
[
[1.0, 1.0],
[1.1, 2.0],
[0.9, 3.0],
[2.0, 2.9],
[3.0, 3.0],
]
)
ax2.plot(points[:, 0], points[:, 1])
tolerance = 0.5
points2 = approximate_polygon(points, tolerance=tolerance)
ax2.plot(points2[:, 0], points2[:, 1])
if interactive:
plt.show()
@unittest.skipUnless(interactive, "ignore plotting in routine tests")
def test_plot_line(self):
"""straightens lines by Douglas Peucker and plots"""
nx_graph = self.nx_graph_arrows1
tolerance = 2
lines = [
[(21, 24), (22, 24), (23, 24), (24, 25)],
[(10, 12), (11, 13), (12, 13), (12, 18), (13, 14), (13, 15), (16, 18), (17, 18), (18, 20)],
[(0, 2), (1, 4), (2, 4), (2, 3), (2, 7), (4, 5), (4, 6)],
[(8, 19), (9, 19), (19, 26)]
]
AmiEdge.plot_all_lines(nx_graph, lines, tolerance)
def test_plot_lines_with_nodes(self, interactive=interactive):
"""adds nodes straightens lines by Douglas Peucker and plots"""
nx_graph = self.nx_graph_arrows1
tolerance = 2
lines = [
[(21, 24), (22, 24), (23, 24), (24, 25)],
[(10, 12), (11, 13), (12, 13), (12, 18), (13, 14), (13, 15), (16, 18), (17, 18), (18, 20)],
[(0, 2), (1, 4), (2, 4), (2, 3), (2, 7), (4, 5), (4, 6)],
[(8, 19), (9, 19), (19, 26)]
]
nodes = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 19, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25}
# TODO make this tidying routine universal
if interactive:
# TODO split into line segmentattion and plotting
logger.warning("skipping line segmentation test")
AmiEdge.plot_all_lines(nx_graph, lines, tolerance, nodes=nodes)
def test_prisma(self):
"""extract primitives from partial prisma diagram"""
assert Resources.PRISMA_RAW.exists()
ami_graph = AmiGraph(self.nx_graph_prisma)
islands = ami_graph.get_or_create_ami_islands()
assert len(islands) == 382
big_islands = []
for island in islands:
bbox = island.get_or_create_bbox()
if bbox.get_height() > 40:
big_islands.append(island)
assert len(big_islands) == 6
@unittest.skip("May have broken this")
def test_extract_raw_image(self):
"""extract the raw pixels (not the skeleton) underlying the extracted lines
plot boxes
erode and dilate
"""
self.display_erode_dilate(self.arrows1, self.nx_graph_arrows1, erode=True, dilate=True)
def test_erode_battery(self):
"""extract the raw pixels (not the skeletonm) underlying the extracted lines
plot boxes
erode and dilate
"""
nx_graph = self.nx_graph_battery1
TestAmiGraph.display_erode_dilate(self.battery1_image, nx_graph)
@unittest.skip("Moved to AmiOCR, NYI")
def test_find_bboxes_with_text(self, interact=interactive):
"""find text boxes and remove those with more than one character
so the remaining lines can be analyses
"""
text_boxes = TextBox.find_text_boxes(self.biosynth1_elem)
assert len(text_boxes) == 38
text_boxes1 = []
for text_box in text_boxes:
if TextUtil.is_text_from_tesseract(text_box.text):
assert type(text_box) is TextBox, f"cannot add {type(text_box)} as TextBox"
text_boxes1.append(text_box)
assert len(text_boxes1) > 0, "require non_zero count of text_boxes"
logger.info(f"{__name__} plotting {len(text_boxes1)} text_boxes of type {type(text_boxes1[0])}")
fig, ax = plt.subplots()
AmiGraph.plot_text_box_boxes(self.biosynth1_binary, ax, text_boxes1)
fig.tight_layout()
if interactive:
plt.show()
def test_get_nx_edge_lengths_list_for_node(self):
"""
asserts lengths of edges to node
:return:
"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
edge_length_by_nx_edge = ami_graph.get_nx_edge_lengths_by_edge_list_for_node(24)
assert {"a": 2.000001} == pytest.approx({"a": 2})
assert {"a": 2.01} == pytest.approx({"a": 2}, 0.1)
expected1 = pytest.approx(
{(24, 21): 30.004166377354995, (24, 22): 9.394147114027968, (24, 23): 9.394147114027968,
(24, 25): 12.010412149464313}, 0.001)
assert {(24, 21): 30.00, (24, 22): 9.39, (24, 23): 9.39, (24, 25): 12.01} == expected1
def test_battery1_elements(self):
"""
Create island_node_id_sets using sknw/NetworkX and check basic properties
:return:
"""
# TODO package commands into AmiGraph
ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
Resources.BATTERY1_RAW, interactive=False, reader=Resources.IMAGE_METHOD
)
nx_graph = ami_graph.nx_graph
assert len(nx_graph.nodes) == 647 # multi, iso, ring full
# assert len(nx_graph.nodes) == 569
connected_components = list(nx.algorithms.components.connected_components(nx_graph))
# assert nx.algorithms.components.number_connected_components(nx_graph) == 212 #
assert (
nx.algorithms.components.number_connected_components(nx_graph) == 290
) # multyi iso ring full
connected_components = list(
nx.algorithms.components.connected_components(nx_graph)
)
assert (
type(connected_components) is list
), f"type of connected components should be list"
assert (
type(connected_components[0]) is set and len(connected_components[0]) == 4
), f"components should be sets and first len == 8"
assert type(list(connected_components[0])[0]) is int, f"members should be int"
ami_graph = AmiGraph(nx_graph)
ami_graph.read_nx_graph(nx_graph)
island_node_id_sets = ami_graph.get_or_create_ami_islands()
# assert len(island_node_id_sets) == 212 # multi iso ring full
assert len(island_node_id_sets) == 290
assert type(island_node_id_sets[0]) is AmiIsland
# assert island_node_id_sets[0].node_ids == {0, 9, 4, 5}
assert island_node_id_sets[0].node_ids == {0, 10, 5, 6}
islands = ami_graph.get_or_create_ami_islands()
for island in islands:
bbox = island.get_or_create_bbox()
w = bbox.get_width()
h = bbox.get_height()
if h > 100 or w > 100:
pass
# image = io.imread(Resources.BATTERY1)
def test_battery1square(self):
"""
tests rings using a single square
:return:
"""
# TODO package commands into AmiGraph
ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
Resources.BATTERY1BSQUARE_RAW, interactive=False
)
nx_graph = ami_graph.nx_graph
assert type(nx_graph) is nx.MultiGraph
assert len(nx_graph.nodes) == 3 # multi, iso, ring full (square has an artificial node)
ami_graph = AmiGraph(nx_graph)
ami_graph.read_nx_graph(nx_graph)
island_node_id_sets = ami_graph.get_or_create_ami_islands()
assert len(island_node_id_sets) == 2
assert type(island_node_id_sets[0]) is AmiIsland
assert island_node_id_sets[0].node_ids == {0, 1}
islands = ami_graph.get_or_create_ami_islands()
for island in islands:
bbox = island.get_or_create_bbox()
w = bbox.get_width()
h = bbox.get_height()
# print(f"{__name__}{bbox}")
"""acces edges
EITHER list(nx_graph.edges(0, 1))[0] (the 3rd index is for mUltigraph
OR nx_graph[s][e][0] and then list
I think...
"""
print("edges", nx_graph.edges)
print("======= ----- =======")
print("edges_list", list(nx_graph.edges), len(list(nx_graph.edges)))
print("======= xxxx =======")
print("edges[0]", list(nx_graph.edges)[0], type(list(nx_graph.edges)[0]), len(list(nx_graph.edges)[0]))
print("======= yyyy =======")
print("edges(0, 1)[0]", "tuple->", list(nx_graph.edges(0, 1))[0], type(list(nx_graph.edges(0, 1))[0])) # start
print("======= edges =======")
for (s, e) in nx_graph.edges():
nx_graph[s][e][0]["nxg"] = "foo"
ps = nx_graph[s][e][0][AmiEdge.PTS]
print("ps", type(ps))
print("keys", nx_graph[s][e][0].keys(), nx_graph[s][e][0]["nxg"])
print("points: ", len(ps), ps[:, 1], ps[:, 0])
def test_create_ami_nodes_from_ids(self):
"""wrap node_ids in AmiNodes"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
# Resources.BIOSYNTH1_CROPPED_ARROWS_RAW
# )
ami_graph = self.resources.arrows1_ami_graph
node_ids = [0, 1, 2, 3, 4, 5, 6, 7]
ami_node_list = ami_graph.create_ami_nodes_from_ids(node_ids)
assert 8 == len(ami_node_list)
assert type(ami_node_list[0]) is AmiNode
# utils ----------------
def test_primitives(self, interact=interactive):
"""
analyses a figure with ~15 simple diagrams and returns their analyses
:return:
"""
interactive = False
island_names = [
"thin_zig",
"diag_sq",
"2ring",
"thick_zag",
"line",
"chord",
"phi",
"cross",
"window",
"racket",
"turnip",
"bigo",
"mido",
"babyo",
"rect",
"inrect",
]
ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(
Resources.PRIMITIVES_RAW, interactive=interact
)
nx_graph = ami_graph.nx_graph
assert type(nx_graph) is nx.MultiGraph
assert (
len(nx_graph.nodes) == 42
) # multi, iso, ring full (square has an artificial node)
logger.debug("\nPrimitives: ", nx_graph)
islands = ami_graph.get_or_create_ami_islands()
assert len(islands) == 16
# TODO create as tests
for i, island in enumerate(islands):
cyc = None
# island.get_or_create_bbox()
logger.debug(
"\n",
"******* island:",
i,
island_names[i],
island.get_or_create_bbox(),
island.node_ids,
)
try:
cyc = nx.algorithms.cycles.find_cycle(island.island_nx_graph)
logger.debug(f"cycles {cyc}")
except nx.exception.NetworkXNoCycle:
# only way of trapping acyclic graph
pass
# draw image
AmiImage.pre_plot_image(Resources.PRIMITIVES_RAW, erode_rad=2)
# draw edges by pts
ami_graph.pre_plot_edges(plt.gca())
# draw node by o, len
ami_graph.pre_plot_nodes(plot_ids=True)
# plt.imshow(img, cmap='gray')
if interactive:
plt.show()
@classmethod
def assert_degrees(cls, ami_graph, degree, result_nodes):
"""
tests degree of connectivity of nodes in graph
uses ami_graph.get_nodes_with_degree
:param ami_graph:
:param degree:
:param result_nodes:
:return:
"""
nodes = AmiGraph.get_node_ids_from_graph_with_degree(ami_graph.nx_graph, degree)
assert nodes == result_nodes, f"nodes of degree {degree} should be {result_nodes}"
# ----- edges -----
def test_multigraph_edges(self):
"""
To annotate multiple edges , currently with keys
:return:
"""
nx_graph = nx.MultiGraph()
nx_graph.add_edge(0, 1, foo=3)
nx_graph.add_edge(0, 2, weight=5)
nx_graph.add_edge(0, 2, weight=10)
nx_graph.add_edge(2, 0, weight=15)
assert len(nx_graph.nodes) == 3
assert list(nx_graph.edges(0)) == [(0, 1), (0, 2), (0, 2), (0, 2)]
assert list(nx_graph.edges(1)) == [(1, 0)]
assert list(nx_graph.edges(2)) == [(2, 0), (2, 0), (2, 0)]
edge_list = list(nx_graph.edges.data())
assert edge_list[0] == (0, 1, {"foo": 3})
assert edge_list[1] == (0, 2, {"weight": 5})
assert edge_list[2] == (0, 2, {"weight": 10})
assert edge_list[3] == (0, 2, {"weight": 15})
assert list(nx_graph.edges.data("weight", default=1)) == [
(0, 1, 1),
(0, 2, 5),
(0, 2, 10),
(0, 2, 15),
]
assert list(nx_graph.edges.data(keys=True)) == [
(0, 1, 0, {"foo": 3}),
(0, 2, 0, {"weight": 5}),
(0, 2, 1, {"weight": 10}),
(0, 2, 2, {"weight": 15}),
]
edges = list(nx_graph.edges.data(keys=True))
assert len(edges) == 4
assert edges[0] == (0, 1, 0, {"foo": 3})
key = 2
assert edges[0][key] == 0
assert edges[1][key] == 0
assert edges[2][key] == 1
assert edges[3][key] == 2
def test_whole_image(self):
assert self.nx_graph_biosynth3 is not None
biosynth3_ami_graph = AmiGraph(nx_graph=self.nx_graph_biosynth3)
islands = biosynth3_ami_graph.get_or_create_ami_islands()
assert len(islands) == 436
islands_big = [island for island in islands if island.get_or_create_bbox().min_dimension() > 20]
assert len(islands_big) == 5
def test_whole_image1(self):
"""
analyse min-maximum and max-min of islands
:return:
"""
assert self.nx_graph_biosynth3 is not None
biosynth3_ami_graph = AmiGraph(nx_graph=self.nx_graph_biosynth3)
islands = biosynth3_ami_graph.get_or_create_ami_islands()
assert len(islands) == 436
counts_by_maxdim = {0: 436, 1: 408, 2: 408, 3: 401, 4: 396, 5: 389, 6: 376, 7: 368, 10: 368, 15: 211, 22: 19,
30: 6, 50: 5, 80: 1}
for max_dim in counts_by_maxdim:
islands_big = AmiIsland.get_islands_with_max_dimension_greater_than(max_dim, islands)
assert len(islands_big) == counts_by_maxdim[max_dim]
counts_by_mindim = {0: 42, 1: 51, 2: 79, 3: 102, 4: 115, 5: 149, 6: 169, 7: 182, 8: 236, 9: 323, 10: 352,
15: 423, 22: 432, 30: 435, 50: 435, 100: 435}
for min_dim in counts_by_mindim:
islands_big = AmiIsland.get_islands_with_max_min_dimension(min_dim, islands)
assert len(islands_big) == counts_by_mindim[min_dim]
def test_island_sizes(self):
"""uses mindim, maxdim, to filter in/out islands. etc."""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.YW5003_5_RAW)
ami_graph = self.resources.yw5003_ami_graph
# all islands
islands = ami_graph.get_or_create_ami_islands()
assert len(islands) == 227, f"expected total islands {len(islands)}"
# two largest
islands = ami_graph.get_or_create_ami_islands(mindim=50)
assert len(islands) == 2, f"expected large islands {len(islands)}"
# very small ones (periods, dots, etc.)
islands = ami_graph.get_or_create_ami_islands(maxdim=2)
assert len(islands) == 16, f"very small islands (periods, dots, decimals) {len(islands)}"
# all thin , including dots
islands = ami_graph.get_or_create_ami_islands(maxmindim=3)
assert len(islands) == 49, f"very thin islands (sans-serif l, i, etc) {len(islands)}"
# long thin , excluding dots
islands = ami_graph.get_or_create_ami_islands(minmaxdim=19)
assert len(islands) == 22, f"thin long islands (sans-serif l, i, etc) {len(islands)}"
# long thin , excluding dots
islands = ami_graph.get_or_create_ami_islands(minmaxdim=24)
assert len(islands) == 9, f"very thin long islands (sans-serif l, i, etc) {len(islands)}"
# islands with no thin dimension
islands = ami_graph.get_or_create_ami_islands(mindim=15)
assert len(islands) == 21, f"chunky islands (H M O etc and the 2 boxes) {len(islands)}"
def test_graph_plots(self):
"""uses mindim, maxdim, to filter in/out islands. etc.
then finds horizontal, vertical and other cnnectiosn between nodes
"""
# NOTE these tests seem correct but pixel-fragile
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.YW5003_5_RAW)
ami_graph = self.resources.yw5003_ami_graph
# second largest island is a boxed plot
# all islands
islands = ami_graph.get_or_create_ami_islands(mindim=50, maxmindim=300)
assert len(islands) == 1, f"expected single islands {len(islands)}"
small_plot = islands[0]
node_ids = small_plot.node_ids
assert len(node_ids) == 36, f"nodes in small graph {len(node_ids)}"
# node_ids are arbitrary
assert node_ids == {258, 132, 389, 136, 24, 288, 546, 36, 40, 424, 46, 177, 569, 63, 448, 193,
323, 590, 591, 592, 593, 594, 595, 596, 86, 605, 606, 607, 608, 609, 354,
101, 103, 487, 114, 510}, f"found {node_ids}"
assert small_plot.nx_edges == [
(258, 323, 0), (132, 177, 0), (389, 448, 0), (136, 177, 0), (136, 193, 0), (24, 36, 0), (24, 36, 1),
(24, 40, 0),
(288, 323, 0), (288, 354, 0), (546, 569, 0), (546, 595, 0), (36, 46, 0), (40, 46, 0), (40, 63, 0),
(424, 448, 0),
(424, 487, 0), (46, 86, 0), (177, 258, 0), (569, 590, 0), (63, 86, 0), (63, 101, 0), (448, 510, 0),
(193, 258, 0),
(193, 288, 0), (323, 389, 0), (590, 591, 0), (590, 608, 0), (591, 592, 0), (591, 605, 0), (592, 593, 0),
(592, 606, 0),
(593, 594, 0), (593, 596, 0), (594, 595, 0), (594, 607, 0), (595, 609, 0), (86, 103, 0), (354, 389, 0),
(354, 424, 0),
(101, 103, 0), (101, 114, 0), (103, 132, 0), (487, 510, 0), (487, 546, 0), (114, 132, 0), (114, 136, 0),
(510, 569, 0)], \
f"found {small_plot.nx_edges}"
pixel_error = 2
# I have struggled to find the right term. "axial" suggests the actual axis
horizontal_lines, vertical_lines, non_hv_lines = \
ami_graph.extract_aligned_node_lists(node_ids, pixel_error)
horiz_line_coord_pairs = str([
[[66, 758], [107, 759]],
[[107, 759], [149, 759]],
[[149, 759], [191, 759]],
[[191, 759], [232, 759]],
[[232, 759], [274, 759]]
])
assert str(horizontal_lines) == horiz_line_coord_pairs, f"horizontal lines should be {horiz_line_coord_pairs}"
vert_line_coord_pairs = str([
[[66, 462], [66, 520]],
[[66, 355], [66, 408]],
[[66, 577], [66, 632]],
[[295, 372], [295, 427]],
[[295, 96], [295, 151]],
[[295, 483], [295, 542]],
[[66, 131], [66, 185]],
[[295, 151], [295, 206]],
[[295, 598], [295, 655]],
[[66, 185], [66, 241]],
[[66, 408], [66, 462]],
[[66, 752], [66, 758]],
[[295, 206], [295, 267]],
[[66, 632], [66, 692]],
[[295, 427], [295, 483]],
[[66, 520], [66, 577]],
# [[66, 758], [65, 770]],
[[107, 759], [107, 764]],
[[149, 759], [149, 764]],
[[191, 759], [191, 762]],
[[232, 759], [232, 764]],
[[274, 759], [274, 770]],
[[66, 241], [66, 300]],
[[295, 542], [295, 598]],
[[295, 267], [295, 324]],
[[66, 300], [66, 355]],
[[295, 655], [295, 715]],
[[295, 324], [295, 372]],
[[66, 692], [66, 752]]
])
assert str(vertical_lines) == vert_line_coord_pairs, f"vertical lines should be {vert_line_coord_pairs}"
non_horvert_node_ids = str([
[[295, 372], [66, 408]], [[295, 96], [66, 131]], [[295, 483], [66, 520]], [[295, 715], [66, 752]],
[[295, 715], [274, 759]], [[295, 151], [66, 185]], [[295, 598], [66, 632]], [[295, 206], [66, 241]],
[[295, 427], [66, 462]], [[66, 758], [65, 770]], [[295, 542], [66, 577]], [[295, 267], [66, 300]],
[[295, 655], [66, 692]],
[[295, 324], [66, 355]]])
assert str(non_hv_lines) == non_horvert_node_ids, f"non-axial lines should be {non_hv_lines}"
def test_enumerate_unique_edges(self):
"""separates 3- connected nodes into separate lines """
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.YW5003_5_RAW)
ami_graph = self.resources.yw5003_ami_graph
small_plot_island_0 = ami_graph.get_or_create_ami_islands(mindim=50, maxmindim=300)[0]
triply_connected_ids = AmiGraph.get_node_ids_from_graph_with_degree(small_plot_island_0.island_nx_graph, 3)
assert len(triply_connected_ids) == 30, f"found {len(triply_connected_ids)}"
unique_ami_edges, multibranches = ami_graph.get_unique_ami_edges_and_multibranches(triply_connected_ids)
assert len(unique_ami_edges) == 48, f"should be {len(unique_ami_edges)}"
assert len(multibranches) == 2, f"should be {len(multibranches)} multibranches"
def test_analyze_topology(self):
"""merges short horizontal and verstical lines from sknw
"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.YW5003_5_RAW)
ami_graph = self.resources.yw5003_ami_graph
small_plot_island = ami_graph.get_or_create_ami_islands(mindim=50, maxmindim=300)[0]
node_ids = small_plot_island.node_ids
ami_edges, multibranches = ami_graph.get_unique_ami_edges_and_multibranches(node_ids)
assert len(ami_edges) == 48, f"expected edge count {len(ami_edges)}"
# ami_nodes = ami_graph.create_ami_nodes_from_ids(node_ids)
edge_tool = AmiEdgeTool.create_tool(ami_graph, ami_edges=ami_edges)
assert edge_tool is not None
assert len(edge_tool.ami_nodes) == 36, f"expected {len(edge_tool.ami_nodes)} nodes in edge_tool"
new_ami_nodes, new_ami_edges = edge_tool.analyze_topology()
assert len(new_ami_nodes) == 36 and len(new_ami_edges) == 48, \
f"nodes {len(new_ami_nodes)} edges {len(new_ami_edges)}"
def test_create_straight_edges(self):
"""tests straightness between nodes (horiz and vert)
"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.YW5003_5_RAW)
ami_graph = self.resources.yw5003_ami_graph
small_plot_island = ami_graph.get_or_create_ami_islands(mindim=50, maxmindim=300)[0]
node_ids = small_plot_island.node_ids
pixel_error = 2
horizontal_lines, vertical_lines, non_hv_lines = ami_graph.extract_aligned_node_lists(node_ids, pixel_error)
for vertical_line in vertical_lines:
print(f"vline {vertical_line}")
edges = small_plot_island.create_nx_edges()
for edge in edges:
print(f"edge {edge}")
def test_create_line_segments(self):
"""segments the edge into straight-lines (AmiLine) and finds axially aligned corners
"""
# ami_graph = AmiGraph.create_ami_graph_from_arbitrary_image_file(Resources.YW5003_5_RAW)
ami_graph = self.resources.yw5003_ami_graph
small_plot_island = ami_graph.get_or_create_ami_islands(mindim=50, maxmindim=300)[0]
ami_edges = small_plot_island.get_or_create_ami_edges()
assert len(ami_edges) == 48, f"found {len(ami_edges)}"
tolerance = 2